NonSpliced RNAseq workflow Version 1
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Download RO CrateWorkflow for NonSpliced RNAseq data with multiple aligners.
Steps:
- workflow_quality.cwl:
- FastQC (control)
- fastp (trimming)
- bowtie2 (read mapping)
- sam_to_sorted-bam
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| threads | number of threads | number of threads to use for computational processes |
|
| memory | Max memory | maximum memory usage in megabytes |
|
| filter_rrna | Filer rRNA | Filter rRNA from reads if true |
|
| prefix_id | Filename prefix | Prefix of the output filenames. |
|
| forward_reads | forward reads | forward sequence file locally |
|
| reverse_reads | reverse reads | reverse sequence file locally |
|
| bowtie2-indexfolder | bowtie2 index | Folder location of the bowtie2 index files. |
|
| kallisto-indexfolder | kallisto index | Folder location of the kallisto index file. |
|
| gtf | GTF file | GTF file location |
|
Steps
| ID | Name | Description |
|---|---|---|
| quality | Quality and filtering workflow | Quality assessment of illumina reads with rRNA filtering option |
| bowtie2 | bowtie2 | runs bowtie2 alignment on the genome with the quality filtered reads. |
| sam_to_sorted-bam | sam to sorted bam | Converts a SAM file to a sorted BAM file |
| featurecounts | FeatureCounts | Calculates gene counts with bowtie2 mapped data and input GTF file with FeatureCounts. |
| kallisto | kallisto | Calculates transcript abundances |
| bowtie2_files_to_folder | bowtie2 output | Preparation of bowtie2 output files to a specific output folder |
| featurecounts_files_to_folder | FeatureCounts output | Preparation of FeatureCounts output files to a specific output folder |
| kallisto_files_to_folder | FeatureCounts output | Preparation of kallisto output files to a specific output folder |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| files_to_folder_fastqc | FASTQC | Quality reporting by FASTQC |
|
| files_to_folder_filtered | Filtered reads folder | Output folder with filtered reads. |
|
| files_to_folder_bowtie2 | bowtie2 output | bowtie2 mapping results folder. Contains sorted bam file, metrics file and mapping statistics (stdout). |
|
| files_to_folder_featurecounts | FeatureCounts output | FeatureCounts results folder. Contains readcounts, summary and mapping statistics (stdout). |
|
| files_to_folder_kallisto | kallisto output | kallisto results folder. Contains transcript abundances, run info and summary. |
|
Version History
Version 1 (earliest) Created 24th Nov 2020 at 11:05 by Bart Nijsse
Added/updated 1 files
Open
master533f564
Creators and Submitter
Views: 1330 Downloads: 43
Created: 24th Nov 2020 at 11:05
Last updated: 8th Jun 2021 at 08:32
Last used: 7th Dec 2022 at 00:32
AttributionsNone
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