Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Fall 3 2021 Sep 13 - Sep 24, Fall 4 2021 Sep 27 - Oct 8
Description
Nextflow provides a standard type of RNA-Seq data pipeline called "nf-core/rnaseq" that we can potentially use for processing data in the Pollen PGRP and other related projects.
For example, the following command shows an example of running this pipeline on a "single end" data set, using a reference genome indicated by the "--fasta" option:
nextflow run nf-core/rnaseq -profile conda --singleEnd --reverseStranded --skipTrimming --reads '*.fastq.gz' --fasta 'ftp://ftp.ensembl.org/pub/release-99/fasta/rattus_norvegicus/dna_index/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz' --gtf 'ftp://ftp.ensembl.org/pub/release-99/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.99.gtf.gz' --fc_count_type transcript
One major benefit of using this pipeline is that there is a lot of support for it in the larger bioinformatics community. There's a company (Sequera) that is supporting this and other Nextflow related projects.