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 **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: f42c889734c8f709ad2fd9090493bcaac8326c98

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: ffab5424bb8b5905aecf6f8e2e6387da7f3df562

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

Path: testdata/md5sum_v12.cwl

Branch/Commit ID: 0ad6983898f0d9001fe0f416f97c4d8b940e384a

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

Path: tests/wf/mut.cwl

Branch/Commit ID: d7481d03fa4b5b4630392540f598acfb100b421d

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/rnaseq-pe-dutp.cwl

Branch/Commit ID: ea2a2ab57710fcf067f67305f3dd6ad29094da1a

DNase-seq - map - Filter PCR Artifacts

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/map/filter-pcr-artifacts.cwl

Branch/Commit ID: 81555a89cc2d16bd3ab131a6685a44b44f08f927

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 1249b5d4e23d57ca5e3b8ad6d8e5f10ddb019f68

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/PerformanceSummaryGenome_v0_1_0.cwl

Branch/Commit ID: f7f887b84734a932534ed6a4732a48852e6169d4

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

Path: testdata/workflow_input_sf_expr_array_v1_2.cwl

Branch/Commit ID: 124a08ce3389eb49066c34a4163cbbed210a0355