{"id":34390,"date":"2023-11-22T06:11:36","date_gmt":"2023-11-22T06:11:36","guid":{"rendered":"https:\/\/www.process.st\/templates\/rnaseq-quality-control-process\/"},"modified":"2024-03-05T15:31:10","modified_gmt":"2024-03-05T15:31:10","slug":"rnaseq-quality-control-process","status":"publish","type":"post","link":"https:\/\/www.process.st\/templates\/rnaseq-quality-control-process\/","title":{"rendered":"RNAseq Quality Control Process"},"content":{"rendered":"\n<section id=\"acquiring-the-raw-rnaseq-data\"> \n <h2>Acquiring the raw RNAseq data<\/h2>\n <div class=\"text-content\">\n   In this task, you will acquire the raw RNAseq data needed for the analysis. The raw data is essential as it contains the initial information necessary for downstream analysis. Make sure to obtain the data from a reliable source that provides accurate and high-quality sequencing results. Have you identified the appropriate source to acquire the raw RNAseq data from? \n <\/div> \n <div class=\"select-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Raw data source <\/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      Public database \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      Collaborator \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      In-house sequencing facility \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      Other \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"upload-rnaseq-data\"> \n <h2>Upload RNAseq data<\/h2>\n <div class=\"text-content\">\n   Now that you have acquired the raw RNAseq data, it's time to upload it for further processing. Uploading the data will allow you to access it in the subsequent steps of the workflow. Have you prepared the raw RNAseq data files for upload? \n <\/div> \n <div class=\"multi-choice-content form-field-content\"> \n  <div class=\"form-group\"> <label> Upload type <\/label> <select disabled class=\"form-control\"> <option value=\"\">Multiple options can be selected from this list<\/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      Bulk upload \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      Individual file upload \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"demultiplexing-of-raw-data\"> \n <h2>Demultiplexing of raw data<\/h2>\n <div class=\"text-content\">\n   In this task, you will demultiplex the raw data. Demultiplexing is the process of separating the sequencing reads belonging to different samples based on their unique barcodes or indexes. This step is crucial for downstream analysis as it allows you to assign each read to its corresponding sample. Have you ensured that each sample in the raw data has a unique barcode or index for demultiplexing? \n <\/div> \n <div class=\"multi-select-content form-field-content\"> \n  <div class=\"form-group\"> <label> Demultiplexing requirements <\/label> \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      Barcode or index for each sample is present \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      Demultiplexing software is available \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      Reference mapping file for sample identification \n    <\/div> <\/li> \n  <\/ul> \n <\/div> \n<\/section> \n<section id=\"checking-the-quality-of-raw-data-with-fastqc\"> \n <h2>Checking the quality of raw data with FastQC<\/h2>\n <div class=\"text-content\">\n   To ensure the reliability of the raw RNAseq data, it is essential to assess its quality. FastQC is a widely used tool for quality control analysis of sequencing data. Running FastQC on the raw data will provide valuable information about the sequencing quality, including measures such as per-base sequence quality and GC content. Have you checked the quality of the raw RNAseq data using FastQC? \n <\/div> \n <div class=\"file-field-content form-field-content\"> \n  <div class=\"form-group\"> <label> Raw data FastQC 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=\"trimming-of-low-quality-reads-and-adapter-sequences\"> \n <h2>Trimming of low quality reads and adapter sequences<\/h2> \n<\/section> \n<section id=\"checking-the-quality-of-processed-data-with-fastqc\"> \n <h2>Checking the quality of processed data with FastQC<\/h2> \n<\/section> \n<section id=\"comparing-raw-vs-processed-data-quality-metrics\"> \n <h2>Comparing raw vs processed data quality metrics<\/h2> \n<\/section> \n<section id=\"mapping-reads-to-the-reference-genome-using-star\"> \n <h2>Mapping reads to the reference genome using STAR<\/h2> \n<\/section> \n<section id=\"generating-an-alignment-summary-statistics\"> \n <h2>Generating an alignment summary statistics<\/h2> \n<\/section> \n<section id=\"checking-the-distribution-of-mapped-reads-coverage\"> \n <h2>Checking the distribution of mapped reads coverage<\/h2> \n<\/section> \n<section id=\"evaluation-of-sequencing-depth-and-saturation\"> \n <h2>Evaluation of sequencing depth and saturation<\/h2> \n<\/section> \n<section id=\"inferring-transcript-abundance-using-rsem\"> \n <h2>Inferring transcript abundance using RSEM<\/h2> \n<\/section> \n<section id=\"checking-for-transcriptome-alignment-warnings-or-errors\"> \n <h2>Checking for transcriptome alignment warnings or errors<\/h2> \n<\/section> \n<section id=\"conducting-principal-component-analysis-pca-on-normalized-counts\"> \n <h2>Conducting Principal Component Analysis (PCA) on normalized counts<\/h2> \n<\/section> \n<section id=\"determining-the-differential-gene-expression-using-deseq2\"> \n <h2>Determining the differential gene expression using DESeq2<\/h2> \n<\/section> \n<section id=\"approval-bioinformatician-review-of-the-resultant-gene-list\"> \n <h2>Approval: Bioinformatician Review of the resultant gene list<\/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\">Determining the differential gene expression using DESeq2<\/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=\"validation-of-differential-gene-expression-using-quantitative-pcr\"> \n <h2>Validation of differential gene expression using quantitative PCR<\/h2> \n<\/section> \n<section id=\"interpretation-of-qpcr-results\"> \n <h2>Interpretation of qPCR results<\/h2> \n<\/section> \n<section id=\"approval-supervisor-review-of-final-qc-report\"> \n <h2>Approval: Supervisor Review of final QC report<\/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\">Checking the distribution of mapped reads coverage<\/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","protected":false},"excerpt":{"rendered":"<p>Acquiring the raw RNAseq data In this task, you will acquire the raw RNAseq data needed for the analysis. The raw data is essential as it contains the initial information necessary for downstream analysis. Make sure to obtain the data from a reliable source that provides accurate and high-quality sequencing results. Have you identified the [&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\udd2c","cover_icon_url":"","tasks_count":"19","template_description":"","template_id":"iAo4O6goBlJX4RKtsuhDGw","task_0":"Acquiring the raw RNAseq data","task_slug_0":"acquiring-the-raw-rnaseq-data","task_1":"Upload RNAseq data","task_slug_1":"upload-rnaseq-data","task_2":"Demultiplexing of raw data","task_slug_2":"demultiplexing-of-raw-data","task_3":"Checking the quality of raw data with FastQC","task_slug_3":"checking-the-quality-of-raw-data-with-fastqc","task_4":"Trimming of low quality reads and adapter sequences","task_slug_4":"trimming-of-low-quality-reads-and-adapter-sequences","task_5":"Checking the quality of processed data with 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