{"id":33873,"date":"2023-11-12T05:06:00","date_gmt":"2023-11-12T05:06:00","guid":{"rendered":"https:\/\/www.process.st\/templates\/rnaseqc-rnaseq-metrics-for-quality-control-and-process-optimization\/"},"modified":"2024-03-05T15:15:30","modified_gmt":"2024-03-05T15:15:30","slug":"rnaseqc-rnaseq-metrics-for-quality-control-and-process-optimization","status":"publish","type":"post","link":"https:\/\/www.process.st\/templates\/rnaseqc-rnaseq-metrics-for-quality-control-and-process-optimization\/","title":{"rendered":"RNASEQC: RNAseq Metrics for Quality Control and Process Optimization"},"content":{"rendered":"\n<section id=\"retrieve-raw-sequencing-data-from-storage\"> \n <h2>Retrieve raw sequencing data from storage<\/h2>\n <div class=\"text-content\">\n   This task involves retrieving the raw sequencing data files from the designated storage location. The raw data contains the information obtained from the sequencing process and serves as the starting point for the analysis. Make sure to locate the correct directory or folder and retrieve the files without modifying or moving them. Please confirm the retrieval of the raw data files by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Raw Data Retrieval <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Yes, data retrieved and intact \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No, data not found \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Data retrieval in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Data retrieval delayed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"decompress-the-raw-data-if-compressed\"> \n <h2>Decompress the raw data if compressed<\/h2>\n <div class=\"text-content\">\n   In case the raw sequencing data is compressed, it needs to be decompressed before further analysis can be performed. Compression is commonly done to save storage space and facilitate data transfer. Use the appropriate decompression tool based on the file format to extract the raw data. If the data is already in its uncompressed form, skip this task. Please confirm the decompression process by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Data Decompression <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Decompressed successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Data already in uncompressed form \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Decompression in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Decompression failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"validate-the-integrity-of-raw-data-files\"> \n <h2>Validate the integrity of raw data files<\/h2>\n <div class=\"text-content\">\n   Ensuring the integrity of raw data files is crucial for reliable analysis results. Use a file integrity checking tool to verify the integrity of the raw sequencing data. Checksums or hash values are commonly used to compare the data file against a known value. If the integrity check fails, it indicates data corruption or transmission errors. Please confirm the validation of the raw data file integrity by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Data Integrity Validation <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Data integrity validated \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Data integrity check failed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Validation in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Validation delayed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"convert-raw-data-into-fastq-format\"> \n <h2>Convert raw data into FASTQ format<\/h2>\n <div class=\"text-content\">\n   The raw data obtained from the sequencing process may be in a different format, such as BAM or SAM, which is not suitable for downstream analysis. This task involves converting the raw data into the FASTQ format, which is commonly used for RNA sequencing data. Use a suitable conversion tool or script to perform the conversion. Please confirm the successful conversion of the raw data files to FASTQ format by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Data Conversion to FASTQ <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Data converted to FASTQ successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Data already in FASTQ format \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Conversion in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Conversion failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"perform-quality-control-on-fastq-files\"> \n <h2>Perform quality control on FASTQ files<\/h2>\n <div class=\"text-content\">\n   Performing quality control (QC) on the FASTQ files is essential to assess the overall quality of the sequencing data before further analysis. Use a QC tool or software to generate quality metrics, such as read length distribution, base composition, and per-base quality scores. Review the QC metrics to identify potential issues and confirm if the data meets the quality standards. Please provide your QC report and observations in the field below. \n <\/div> \n <div class=\"textarea-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Quality Control Report and Observations <\/label> <textarea placeholder=\"Something will be typed here...\" rows=\"3\" disabled class=\"form-control\"><\/textarea> \n  <\/div> \n <\/div> \n<\/section> \n<section id=\"trim-lowquality-bases-and-remove-adapter-sequences\"> \n <h2>Trim low-quality bases and remove adapter sequences<\/h2>\n <div class=\"text-content\">\n   To improve the quality of the sequencing data, low-quality bases and adapter sequences need to be trimmed. Low-quality bases can introduce noise into the analysis, while adapter sequences are remnants of the sequencing library preparation process. Use a trimming tool or software to remove these sequences while ensuring the remaining reads are of high quality. Please confirm the successful trimming of low-quality bases and removal of adapter sequences by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Trimming and Adapter Removal <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Trimming and adapter removal successful \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No trimming or removal needed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Trimming in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Trimming failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"align-the-reads-to-the-reference-genome\"> \n <h2>Align the reads to the reference genome<\/h2>\n <div class=\"text-content\">\n   Aligning the reads to a reference genome is a fundamental step in the RNA sequencing analysis pipeline. Use a suitable alignment tool or software to align the reads to the reference genome assembly. The aligned reads provide information on their position in the genome and enable downstream analysis, such as variant calling. Please confirm the successful alignment of the reads to the reference genome by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Read Alignment <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Reads aligned successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No read alignment needed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Alignment in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Alignment failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"sort-aligned-reads-by-coordinate\"> \n <h2>Sort aligned reads by coordinate<\/h2>\n <div class=\"text-content\">\n   Sorting the aligned reads by coordinate is important to ensure efficient downstream analysis. Coordinate sorting arranges the aligned reads based on their genomic positions, facilitating variant calling and other analyses that rely on positional information. Use a suitable sorting tool or software to sort the aligned reads by coordinate. Please confirm the successful sorting of the aligned reads by coordinate by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Read Sorting <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Reads sorted by coordinate successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No read sorting needed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Sorting in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Sorting failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"mark-duplicates-in-the-aligned-reads\"> \n <h2>Mark duplicates in the aligned reads<\/h2>\n <div class=\"text-content\">\n   Duplication of reads can occur during the sequencing process or as a result of library preparation. Marking duplicates is essential to avoid overrepresentation of certain reads in downstream analysis, such as variant calling. Use a duplicates marking tool or software to identify and mark the duplicate reads. Please confirm the successful marking of duplicates in the aligned reads by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Duplicate Marking <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Duplicates marked successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No duplicate marking needed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Marking in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Marking failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"index-the-sorted-bam-files\"> \n <h2>Index the sorted BAM files<\/h2>\n <div class=\"text-content\">\n   Indexing the sorted BAM files allows for rapid retrieval of specific genomic regions. The index file contains positional information that enables efficient random access to the aligned reads. Use a suitable indexing tool or software to create the index file for the sorted BAM files. Please confirm the successful indexing of the sorted BAM files by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of BAM File Indexing <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      BAM files indexed successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No indexing needed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Indexing in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Indexing failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"read-alignment-quality-check\"> \n <h2>Read alignment quality check<\/h2>\n <div class=\"text-content\">\n   Performing a quality check on the read alignment is necessary to ensure the alignment results are accurate and reliable. Use a suitable read alignment quality check tool or software to assess the alignment quality based on various metrics, such as mapping quality scores and alignment statistics. Review the quality check results and confirm if the read alignment meets the desired quality standards. Please provide your quality check report and observations in the field below. \n <\/div> \n <div class=\"textarea-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Read Alignment Quality Check Report and Observations <\/label> <textarea placeholder=\"Something will be typed here...\" rows=\"3\" disabled class=\"form-control\"><\/textarea> \n  <\/div> \n <\/div> \n<\/section> \n<section id=\"recalibrate-base-quality-scores\"> \n <h2>Recalibrate base quality scores<\/h2>\n <div class=\"text-content\">\n   Recalibrating the base quality scores is important to improve the accuracy of variant calling and downstream analyses that rely on base quality information. The base quality scores represent the confidence level of each base call and can be affected by various factors during the sequencing process. Use a suitable base quality score recalibration tool or software to recalibrate the scores based on known variants and quality reference data. Please confirm the successful recalibration of the base quality scores by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Base Quality Score Recalibration <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Base quality scores recalibrated successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No recalibration needed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Recalibration in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Recalibration failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"perform-variant-calling\"> \n <h2>Perform variant calling<\/h2>\n <div class=\"text-content\">\n   Variant calling is the process of identifying genetic variants, such as single nucleotide polymorphisms (SNPs) and insertions\/deletions (indels), compared to the reference genome. Use a suitable variant calling tool or software to perform the variant calling analysis based on the aligned reads. The identified variants provide valuable information for further analysis and interpretation. Please confirm the successful identification of variants by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Variant Calling <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Variants called successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No variant calling needed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Variant calling in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Variant calling failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"annotate-identified-variants\"> \n <h2>Annotate identified variants<\/h2>\n <div class=\"text-content\">\n   Annotating the identified variants with relevant information, such as gene names, functional impact, and population frequency, enhances the interpretation of the results. Use a suitable variant annotation tool or software to annotate the identified variants based on available reference databases or resources. The annotated variants facilitate the identification of biologically relevant variants. Please confirm the successful annotation of the identified variants by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Variant Annotation <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Variants annotated successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No variant annotation needed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Annotation in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Annotation failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"perform-quality-control-on-the-final-results\"> \n <h2>Perform quality control on the final results<\/h2>\n <div class=\"text-content\">\n   Performing quality control (QC) on the final results ensures the reliability and accuracy of the analysis. Use suitable QC tools or software to assess various metrics, such as variant call rate, genotype concordance, and allele frequency distribution. Review the QC metrics to identify any potential issues and confirm if the final results meet the quality standards. Please provide your QC report and observations in the field below. \n <\/div> \n <div class=\"textarea-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Final Results Quality Control Report and Observations <\/label> <textarea placeholder=\"Something will be typed here...\" rows=\"3\" disabled class=\"form-control\"><\/textarea> \n  <\/div> \n <\/div> \n<\/section> \n<section id=\"approval-lab-manager\"> \n <h2>Approval: Lab Manager<\/h2>\n <div class=\"approval-content\"> \n  <div class=\"header\"> \n   <div class=\"list-title\">\n    Will be submitted for approval:\n   <\/div> \n  <\/div> \n  <div class=\"approval-rule-subject-tasks-list\"> \n   <ul class=\"list\"> \n    <li> \n     <div class=\"approval-rule-subject-tasks-list-item\"> \n      <div class=\"item\"> \n       <div class=\"container\"> <span class=\"title\">Perform quality control on the final results<\/span> \n        <div class=\"body\">\n         Will be submitted\n        <\/div> \n       <\/div> \n      <\/div> \n     <\/div> <\/li> \n   <\/ul> \n  <\/div> \n <\/div> \n<\/section> \n<section id=\"generate-reports-for-rnaseqc-metrics\"> \n <h2>Generate reports for RNASEQC metrics<\/h2>\n <div class=\"text-content\">\n   Generating reports for RNASEQC metrics provides a comprehensive summary of the analysis results and facilitates interpretation and sharing with stakeholders. Use a suitable reporting tool or software to generate the RNASEQC metrics report based on the analysis outputs and QC metrics. The report should include relevant information, such as sequencing statistics, alignment metrics, variant calling results, and quality control assessments. Please upload the generated RNASEQC metrics report in the field below. \n <\/div> \n <div class=\"file-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Upload RNASEQC Metrics Report <\/label> \n   <div class=\"file-container\"> <button type=\"button\" disabled class=\"btn btn-default\"> <i class=\"fa fa-upload btn-icon\"><\/i> File will be uploaded here <\/button> \n   <\/div> \n  <\/div> \n <\/div> \n<\/section> \n<section id=\"store-the-rnaseqc-metrics-report-for-future-referencing\"> \n <h2>Store the RNASEQC metrics report for future referencing<\/h2>\n <div class=\"text-content\">\n   Storing the RNASEQC metrics report is important for future referencing and reproducibility of the analysis. Save the generated RNASEQC metrics report in a designated storage location or database. Make sure the report is easily retrievable and properly documented for future use. Please confirm the storage of the RNASEQC metrics report by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Report Storage <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Report stored successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No report storage needed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Storage in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Storage failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"clean-up-temporary-files-created-during-the-process\"> \n <h2>Clean up temporary files created during the process<\/h2>\n <div class=\"text-content\">\n   Cleaning up temporary files created during the analysis process helps free up storage space and maintain a clean and organized workflow. Identify and remove any unnecessary or temporary files generated during the analysis, such as intermediate alignment files or temporary index files. Please confirm the successful cleanup of temporary files by selecting the appropriate option below. \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Confirmation of Temporary File Cleanup <\/label> <select disabled class=\"form-control\"> <option value=\"An option will be selected here\">An option will be selected here<\/option> <\/select> \n  <\/div> \n  <ul class=\"items\"> \n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       1 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Temporary files cleaned up successfully \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       2 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      No temporary file cleanup needed \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       3 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Cleanup in progress \n    <\/div> <\/li>\n   <li class=\"item\"> \n    <div class=\"step-number-container\"> \n     <div class=\"step-number\">\n       4 \n     <\/div> \n    <\/div> \n    <div class=\"step-checkbox-container\"> \n     <div class=\"step-checkbox\"><\/div> \n    <\/div> \n    <div class=\"item-name-static\">\n      Cleanup failed \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section>\n","protected":false},"excerpt":{"rendered":"<p>Retrieve raw sequencing data from storage This task involves retrieving the raw sequencing data files from the designated storage location. The raw data contains the information obtained from the sequencing process and serves as the starting point for the analysis. Make sure to locate the correct directory or folder and retrieve the files without modifying [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"ep_exclude_from_search":false,"cover_icon_emoji":"\ud83d\udcca","cover_icon_url":"","tasks_count":"19","template_description":"","template_id":"lcnB4tr8goafRrVe7kVH9Q","task_0":"Retrieve raw sequencing data from storage","task_slug_0":"retrieve-raw-sequencing-data-from-storage","task_1":"Decompress the raw data if compressed","task_slug_1":"decompress-the-raw-data-if-compressed","task_2":"Validate the integrity of raw data files","task_slug_2":"validate-the-integrity-of-raw-data-files","task_3":"Convert raw data into FASTQ format","task_slug_3":"convert-raw-data-into-fastq-format","task_4":"Perform quality control on FASTQ files","task_slug_4":"perform-quality-control-on-fastq-files","task_5":"Trim low-quality bases and remove adapter sequences","task_slug_5":"trim-lowquality-bases-and-remove-adapter-sequences","task_6":"Align the reads to the reference genome","task_slug_6":"align-the-reads-to-the-reference-genome","task_7":"Sort aligned reads by coordinate","task_slug_7":"sort-aligned-reads-by-coordinate","task_8":"Mark duplicates in the aligned reads","task_slug_8":"mark-duplicates-in-the-aligned-reads","task_9":"Index the sorted BAM files","task_slug_9":"index-the-sorted-bam-files","task_10":"Read alignment quality check","task_slug_10":"read-alignment-quality-check","task_11":"Recalibrate base quality scores","task_slug_11":"recalibrate-base-quality-scores","task_12":"Perform variant calling","task_slug_12":"perform-variant-calling","task_13":"Annotate identified variants","task_slug_13":"annotate-identified-variants","task_14":"Perform quality control on the final results","task_slug_14":"perform-quality-control-on-the-final-results","task_15":"Approval: Lab Manager","task_slug_15":"approval-lab-manager","task_16":"Generate reports for RNASEQC metrics","task_slug_16":"generate-reports-for-rnaseqc-metrics","task_17":"Store the RNASEQC metrics report for future referencing","task_slug_17":"store-the-rnaseqc-metrics-report-for-future-referencing","task_18":"Clean up temporary files created during the process","task_slug_18":"clean-up-temporary-files-created-during-the-process","task_19":"","task_slug_19":"","task_20":"","task_slug_20":"","task_21":"","task_slug_21":"","task_22":"","task_slug_22":"","task_23":"","task_slug_23":"","task_24":"","task_slug_24":"","task_25":"","task_slug_25":"","task_26":"","task_slug_26":"","task_27":"","task_slug_27":"","task_28":"","task_slug_28":"","task_29":"","task_slug_29":"","task_30":"","task_slug_30":"","task_31":"","task_slug_31":"","task_32":"","task_slug_32":"","task_33":"","task_slug_33":"","task_34":"","task_slug_34":"","task_35":"","task_slug_35":"","task_36":"","task_slug_36":"","task_37":"","task_slug_37":"","task_38":"","task_slug_38":"","task_39":"","task_slug_39":"","task_40":"","task_slug_40":"","task_41":"","task_slug_41":"","task_42":"","task_slug_42":"","task_43":"","task_slug_43":"","task_44":"","task_slug_44":"","task_45":"","task_slug_45":"","task_46":"","task_slug_46":"","task_47":"","task_slug_47":"","task_48":"","task_slug_48":"","task_49":"","task_slug_49":"","task_50":"","task_slug_50":"","task_51":"","task_slug_51":"","task_52":"","task_slug_52":"","task_53":"","task_slug_53":"","task_54":"","task_slug_54":"","task_55":"","task_slug_55":"","task_56":"","task_slug_56":"","task_57":"","task_slug_57":"","task_58":"","task_slug_58":"","task_59":"","task_slug_59":"","task_60":"","task_slug_60":"","task_61":"","task_slug_61":"","task_62":"","task_slug_62":"","task_63":"","task_slug_63":"","task_64":"","task_slug_64":"","task_65":"","task_slug_65":"","task_66":"","task_slug_66":"","task_67":"","task_slug_67":"","task_68":"","task_slug_68":"","task_69":"","task_slug_69":"","task_70":"","task_slug_70":"","task_71":"","task_slug_71":"","task_72":"","task_slug_72":"","task_73":"","task_slug_73":"","task_74":"","task_slug_74":"","task_75":"","task_slug_75":"","task_76":"","task_slug_76":"","task_77":"","task_slug_77":"","task_78":"","task_slug_78":"","task_79":"","task_slug_79":"","task_80":"","task_slug_80":"","task_81":"","task_slug_81":"","task_82":"","task_slug_82":"","task_83":"","task_slug_83":"","task_84":"","task_slug_84":"","task_85":"","task_slug_85":"","task_86":"","task_slug_86":"","task_87":"","task_slug_87":"","task_88":"","task_slug_88":"","task_89":"","task_slug_89":"","task_90":"","task_slug_90":"","task_91":"","task_slug_91":"","task_92":"","task_slug_92":"","task_93":"","task_slug_93":"","task_94":"","task_slug_94":"","task_95":"","task_slug_95":"","task_96":"","task_slug_96":"","task_97":"","task_slug_97":"","task_98":"","task_slug_98":"","task_99":"","task_slug_99":"","footnotes":""},"categories":[26,114],"tags":[],"class_list":["post-33873","post","type-post","status-publish","format-standard","hentry","category-quality-control","category-supply-chain-management"],"acf":[],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/www.process.st\/templates\/wp-json\/wp\/v2\/posts\/33873","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.process.st\/templates\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.process.st\/templates\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.process.st\/templates\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.process.st\/templates\/wp-json\/wp\/v2\/comments?post=33873"}],"version-history":[{"count":0,"href":"https:\/\/www.process.st\/templates\/wp-json\/wp\/v2\/posts\/33873\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.process.st\/templates\/wp-json\/wp\/v2\/media?parent=33873"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.process.st\/templates\/wp-json\/wp\/v2\/categories?post=33873"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.process.st\/templates\/wp-json\/wp\/v2\/tags?post=33873"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}