Question

Import RSEM output without sample data

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Luisa • 0

@861b563d

Last seen 2.8 years ago

Japan

Hi,

I just want to ask if it is possible to import RSEM output to DESeq2 without the sample file. I don't know why but I do not have it for this particular data.

Or If is it a way to transform the data from RSEM to be able to used in DESeq2 without the sample?

Thank you!

DESeq2 tximportData tximport • 1.2k views

ADD COMMENT • link updated 2.8 years ago by Michael Love 43k • written 2.9 years ago by Luisa • 0

score 1 · Answer 1 · 2022-02-10

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Michael Love 43k

@mikelove

Last seen 1 day ago

United States

The tximport pipeline is really designed for the original sample file, but if you want to ignore issues with gene length changing across samples, you could take the rounded counts. This is then ignoring the effective gene lengths that tximport uses as an offset, so it would be different than what you would get with the original sample files.

ADD COMMENT • link 2.9 years ago Michael Love 43k

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Hi, I understand, however seems difficult to find the sample file.

If I made the rounded counts, which step/command could I procede with Deseq2?

ADD REPLY • link 2.9 years ago Luisa • 0

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Check the DESeq2 vignette and workflow, we've spent a lot of time building these to address questions like this.

ADD REPLY • link 2.8 years ago Michael Love 43k