Question: using tximport with STAR transcript-quantification output
0
gravatar for mohamedrefaat.1.1992
6 weeks ago by
mohamedrefaat.1.19920 wrote:

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

deseq2 star tximport • 88 views
ADD COMMENTlink modified 6 weeks ago by Michael Love26k • written 6 weeks ago by mohamedrefaat.1.19920
Answer: using tximport with STAR transcript-quantification output
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gravatar for Michael Love
6 weeks ago by
Michael Love26k
United States
Michael Love26k wrote:

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"

ADD COMMENTlink written 6 weeks ago by Michael Love26k
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