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Showing results for "rnaseq" (Show all)

Graph Name Retrieved From View
workflow graph rnaseq-header.cwl

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

Path: metadata/rnaseq-header.cwl

Branch/Commit ID: 657eb494c880480574ac111dab4e11a06453d168
workflow graph gatk4W-spark.cwl

Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in This is a proposed standard operating procedure for genomic variant detection using GATK4. It is hoped to be effective and useful for getting SARS-CoV-2 genome variants. It uses Illumina RNASEQ reads and genome sequence.

https://github.com/ambarishK/bio-cwl-tools.git

Path: gatk4W-spark.cwl

Branch/Commit ID: fcab170f3e8a4bc70601650401cce2a9df42f484
workflow graph Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

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

Path: definitions/pipelines/pvacseq.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph xenbase-rnaseq-pe.cwl

XenBase workflow for analysing RNA-Seq paired-end data

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

Path: workflows/xenbase-rnaseq-pe.cwl

Branch/Commit ID: 2d00e7f29c72d33b70dcd46b58db1fc31a7f2d86
workflow graph TOPMed_RNA-seq

TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/README.md). Example input files: [Dockstore.json](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/rnaseq_pipeline_fastq-example.yml). Quickstart instructions are [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/README.md#Quick Start). [GitHub Repo](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL) Pipeline steps: 1. Align RNA-seq reads with [STAR v2.5.3a](https://github.com/alexdobin/STAR). 2. Run [Picard](https://github.com/broadinstitute/picard) [MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates). 2a. Create BAM index for MarkDuplicates BAM with [Samtools 1.6](https://github.com/samtools/samtools/releases) index. 3. Transcript quantification with [RSEM 1.3.0](https://deweylab.github.io/RSEM/) 4. Gene quantification and quality control with [RNA-SeQC 1.1.9](https://github.com/francois-a/rnaseqc)

https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL.git

Path: workflow/rnaseq_pipeline_fastq.cwl

Branch/Commit ID: 06c6ff20f4e719d7f7224c17b22dce8617e92447
workflow graph rnaseq-header.cwl

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

Path: metadata/rnaseq-header.cwl

Branch/Commit ID: 09c08f858e91c4cfd387067f07445722ac7e18aa
workflow graph xenbase-rnaseq-pe.cwl

XenBase workflow for analysing RNA-Seq paired-end data

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

Path: workflows/xenbase-rnaseq-pe.cwl

Branch/Commit ID: 94471ee6c01b7bc17102e45e56e7366c2a52acdf
workflow graph rnaseq-header.cwl

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

Path: metadata/rnaseq-header.cwl

Branch/Commit ID: 62323c137c0ce9b3f843df0dfbda28dafa7c90cf
workflow graph rnaseq_metrics_workflow.cwl

https://github.com/NCI-GDC/gdc-rnaseq-cwl.git

Path: workflows/subworkflows/rnaseq_processing/rnaseq_metrics_workflow.cwl

Branch/Commit ID: f0594206c230e53ad3ad9de14364fc6bce1d5cb7
workflow graph Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

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

Path: definitions/subworkflows/pvacseq.cwl

Branch/Commit ID: 9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f