rnaseq-pipeline
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PavlidisLab
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
This way, we could remove the trimmed reads without having to rerun the whole pipeline if we need to regenerate QC reports.
This feature has been added to MultiQC 1.25 as part of https://github.com/MultiQC/MultiQC/pull/2794. There are some basic conventions, but we could generate settings so that we can preserve SRX/SRR identifiers.
Having to download whole FASTQs is not necessary for the purpose of getting batch information, since we only need to grab the header from any read. fastq-dump can do that...
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RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.