Dear Dr. Patro, developers of Salmon and BioC community,
I have put great amount of effort to find out answer to this question on internet. Couldn't find it anywhere (bioconductor, biostars, seqanswers, github etc.).
I have 3 replicates for each sample and one of the replicates from each sample is single-end and other two are paired-end as SE and PE were processed at different facilities (I know I have to do batch correction in downstream analysis). Now I want to use transcript level abundance from quant.sf file which I derived for each replicates using Salmon's quasi-mapping pipeline (used appropriate flags for SE and PE reads). All these (SE & PE) reads are strand specific.
My question is, can I use quant.sf directly from these replicates for downstream DE analysis using tximport or do SE or PE requires separate kind of processing before I can use them together as replicates for downstream analysis. I am planning to use limma-voom for my DE analysis.
Thank you so much for your time and apologies if the question was answered already.