Question: samples.txt?how to generate
gravatar for Daria
3 months ago by
Daria0 wrote:

I have 3 control and 3 experiment samples and quant.sf files for all of them. I would like to run deseq, however I have no idea how to create samples.txt and can't figure it out from tximport documentation.

deseq2 • 51 views
ADD COMMENTlink modified 3 months ago by James W. MacDonald51k • written 3 months ago by Daria0
Answer: samples.txt?how to generate
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald51k wrote:

You don't really need a file called samples.txt. You just need a data.frame that contains columns that describe pertinent information about your samples, where the row.names of the data.frame are the same as your samples. You could recreate the data.frame used in the DESeq2 vignette like this:

> samps <- paste0("ERR", 188000 + c(297, 88,329, 288, 21, 356))
> samps 
[1] "ERR188297" "ERR188088" "ERR188329" "ERR188288" "ERR188021" "ERR188356"
> z <-  data.frame(pop = rep("TSI", 6), center = rep("UNIGE", 6), run = samps, condition = rep(c("A","B"), each = 3), row.names = samps)
> z
          pop center       run condition
ERR188297 TSI  UNIGE ERR188297         A
ERR188088 TSI  UNIGE ERR188088         A
ERR188329 TSI  UNIGE ERR188329         A
ERR188288 TSI  UNIGE ERR188288         B
ERR188021 TSI  UNIGE ERR188021         B
ERR188356 TSI  UNIGE ERR188356         B

And you could then proceed as per the vignette. You would obviously need to do something tailored to your experiment, but that's the idea.

ADD COMMENTlink written 3 months ago by James W. MacDonald51k
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