Up to date bulk RNA-seq Quality Control tools?


EDIT: I think mutliQC might be the answer: github.com/COMBINE-lab/salmon/issues/252#issuecomment-405442271

Hey ya'll,

I am using going from fastq.gz SRR files to, ultimately a gene expression matrix I can use within DeSeq2 and/or edgeR

I was guided by a great few people to use salmon. You know who you are : )

The snakemake/salmon pipeline is done, however I was wondering if QC is required prior to plugging the fastq's into salmon.

I was reading here: Adapter trimming before mapping with Salmon and it refers to the github for salmon, where QC is recommended.

And if QC is required to trim adapters/remove low quality reads, could someone share what tools are recommended for my current salmon/snakemake pipeline, please?

Here is a post I found which recommends multiQC, however multiQC looks like an all-in-one package.

Looking for appropriate software QC for bulk RNA seq.

Thank you in advance : )




MultiQC acts as an aggregator of FastQC results so you need to run FastQC on all samples before MultiQC.

before adding your answer.

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