Up to date bulk RNA-seq Quality Control tools?

Question

[Pratik]

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

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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 : )

Answer 1

[GenoMax]

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

[Pratik]

Thank you Genomax : )

Answer 2

[jared.andrews07]

If you don't want to deal with installing stuff or building your own pipeline, you can use the nf-core RNA-seq pipeline, which is community curated/built and has a number of options. It uses salmon by default and runs about every QC tool you could ever need and has a nice multiQC summary at the end. It'll take care of adapter/quality trimming for you as well, via TrimGalore.

[Pratik]

Thank you Jared.Andres07 : )

Bookmarked.