Explore Workflows

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-read** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

https://github.com/datirium/workflows.git

Path: workflows/rnaseq-se.cwl

Branch/Commit ID: e238d1756f1db35571e84d72e1699e5d1540f10c

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/scatter-valuefrom-wf5.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/panel_of_normals.cwl

Branch/Commit ID: 3f3b186da9bf82a5e2ae74ba27aef35a46174ebe

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines15-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/search.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b

Packed ID: main

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl

Branch/Commit ID: 9c0b1497c467393e1a54735575043dced73e95c4

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/js-expr-req-wf.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4

Packed ID: wf

https://github.com/common-workflow-language/common-workflow-language.git

Path: v1.0/v1.0/count-lines4-wf.cwl

Branch/Commit ID: 4fd45edb9531a03223c18a586e32d0baf0d5acb2

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl

Branch/Commit ID: e59c77629936fad069007ba642cad49fef7ad29f