Spliced RNAseq workflow Version 1
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Download RO-CrateWorkflow for Spliced RNAseq data Steps:
- workflow_quality.cwl:
- FastQC (Read Quality Control)
- fastp (Read Trimming)
- STAR (Read mapping)
- 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 | int? |
| memory | maximum memory usage in megabytes | maximum memory usage in megabytes | int? |
| filter_rrna | n/a | n/a | boolean |
| prefix_id | n/a | prefix of the filename outputs | string |
| forward_reads | forward reads | forward sequence file locally | File |
| reverse_reads | reverse reads | reverse sequence file locally | File |
| STAR-indexfolder | folder where the STAR indices are | n/a | Directory |
| kallisto-indexfolder | folder where the kallisto indices are | n/a | Directory? |
| gtf | n/a | gtf file | File |
| quantMode | n/a | Run with get gene quantification | {"type"=>"enum", "symbols"=>["None", "TranscriptomeSAM", "GeneCounts"]} (Optional) |
Steps
| ID | Name | Description |
|---|---|---|
| quality | Quality and filtering workflow | Quality assessment of illumina reads with rRNA filtering option |
| STAR | STAR | runs STAR alignment on the genome with the quality filtered reads. |
| featurecounts | FeatureCounts | Calculates gene counts with bowtie2 mapped data and input GTF file with FeatureCounts. |
| kallisto | kallisto | Calculates transcript abundances |
| STAR_files_to_folder | STAR output | Preparation of STAR 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 | kallisto 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 | Directory |
| files_to_folder_filtered | Filtered reads folder | Output folder with filtered reads. | Directory |
| files_to_folder_STAR | STAR output folder | STAR results folder. Contains logs, bam file, readcounts per gene and splice_junctions. | Directory |
| files_to_folder_featurecounts | FeatureCounts output | FeatureCounts results folder. Contains readcounts, summary and mapping statistics (stdout). | Directory |
| files_to_folder_kallisto | kallisto output | kallisto results folder. Contains transcript abundances, run info and summary. | Directory |
Creators and Submitter
Views: 463 Downloads: 34
Created: 22nd Dec 2020 at 15:53
Last updated: 8th Jun 2021 at 13:31
Last used: 17th Oct 2021 at 03:56
AttributionsNone
Version History
Version 1 Created 22nd Dec 2020 at 15:53 by Bart Nijsse
No revision comments
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https://orcid.org/0000-0001-8172-8981
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