Explore Workflows

https://chipster.csc.fi/manual/library-type-summary.html Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. 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 files 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/trim-rnaseq-pe-smarter-dutp.cwl

Branch/Commit ID: 00ea05e22788029370898fd4c17798b11edf0e57

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: d2c2f2eb846ae2e9cdcab46e3bb88e42126cb3f5

Compare simulated and measured pedestal events (exposed to night-sky background light and with closed camera lid).

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

Path: workflows/ValidatePedestalEvents.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7

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

Path: tests/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

Packed ID: main

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

Path: tests/io-file-default-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

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

Path: testdata/workflow_input_format_expr_v1_2.cwl

Branch/Commit ID: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51

Motif Finding with HOMER with target and background regions from peaks --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis-peak.cwl

Branch/Commit ID: 00ea05e22788029370898fd4c17798b11edf0e57

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

Path: tests/conditionals/cond-with-defaults.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

https://github.com/ncbi/pgap.git

Path: task_types/tt_checkm_wnode.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb

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

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: c602e3cdd72ff904dd54d46ba2b5146eb1c57022