salmon - tximport - deseq2 gene level workflow
I am applying salmon quant with --geneMap option to quantify RNA-SEQ to gene level count files. I plan to proceed with DE using Deseq2.
Is it OK to use txIn and txOut in tximport as follows:
tximport(files, type="salmon", countsFromAbundance="no", txIn=T , txOut=T ).
In other words, apply the gene count files as if these are transcripts and avoid any upper level aggregation. I did not find the natural way of applying gene counts to tximport.
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Why don't you make it as simple as possible and run
salmonwith the default parameters on your fastq files, followed by standardtximportto aggregate tx to gene level?I believe there is contamination on one chromosome (M) which I want to get rid off after alignment but before DE. It's easier to do on the gene level right after
Salmon. There are other ways to do that, but I thoughttximporton gene level would be straightforward.