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thelovelab / tximport

Transcript quantification import for modular pipelines
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import using tximport for the rsem count table to get integers? #52

Closed marwa38 closed 1 year ago

marwa38 commented 1 year ago

The rsem table doesn't have integers so it is common to use tximport before running differential gene expression downstream analysis. I am wondering what tximport do in rsem table? what kind of modification? I am trying to use SARTools (deseq2 method) to get my differential expressed genes but the input count table needs to be an integer so I was thinking of just using round() as I am not sure what tximport modification is doing for the rsem table.

mikelove commented 1 year ago

In short tximport->DESeq2 pipeline rounds the fractional pieces to integers.

marwa38 commented 1 year ago

I can't just use round()?

mikelove commented 1 year ago

Yes you can use round.