Question: salmon - tximport - deseq2 gene level workflow
gravatar for jomo018
2.3 years ago by
jomo018610 wrote:

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.

rna-seq salmon deseq2 tximport • 1.2k views
ADD COMMENTlink written 2.3 years ago by jomo018610

Why don't you make it as simple as possible and run salmon with the default parameters on your fastq files, followed by standard tximport to aggregate tx to gene level?

ADD REPLYlink written 2.3 years ago by ATpoint46k

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 thought tximport on gene level would be straightforward.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by jomo018610
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