Question

using tximport with STAR transcript-quantification output

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mohamedrefaat.1.1992 • 0

@mohamedrefaat11992-22243

Last seen 2.4 years ago

Austria

Hi,

is it possible to calculate gene-level count using transcript-quantification files generated by other software not currently supported by tximport?

Basically, I have transcript-level quantification files that were generated using STAR and I want to calculate gene-level abundance to be able to use DESeq2 downstream.

Best, Mohamed

tximport deseq2 STAR • 2.8k views

ADD COMMENT • link updated 17 months ago by rodrigo.duarte88 ▴ 40 • written 6.0 years ago by mohamedrefaat.1.1992 • 0

score 1 · Answer 1 · 2024-06-06

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rodrigo.duarte88 ▴ 40

@rodrigoduarte88-16306

Last seen 17 months ago

United States

Please note that STAR can calculate gene-level expression if you use the flag "--quantMode GeneCounts".

ADD COMMENT • link 17 months ago rodrigo.duarte88 ▴ 40

score 0 · Answer 2 · 2019-10-30

Yes, you can, there are the following arguments (from ?tximport)

geneIdCol - name of column with gene id. if missing, the tx2gene argument can be used txIdCol - name of column with tx id abundanceCol - name of column with abundances (e.g. TPM or FPKM) countsCol - name of column with estimated counts lengthCol - name of column with feature length information

You just have to specify these, and say type="none"