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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Sprint:Summer 2, Summer 3, Summer 4, Summer 6
Description
Task: Continue the workflow started in IGBF-3708 by running the latest version of the nf-core/rnaseq pipeline with the downloaded fastq files. Continue to document the commands used to run this pipeline (see IGBF-3721).
For reference, here is that workflow once again:
Run prefetch.sh to get .sra files for the list of SRR accessions.Check that the .sra files got downloaded correctly.Run fasterq-dump to make fastq files from the .sra files.Compress the fastq files with gzip using gzip.sh and submit to slurm queue using sbatch-doIt.sh- Run nf-core/rnaseq pipeline latest version. For this, you have to make a "parameter" file and provide gene annotations (.gtf file), genome annotations (.bed file), and genome assembly (.fasta file).
- Check that the pipeline ran correctly.