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