Getting samples.txt to use in the salmon to DESeq2 pipeline

Question

[Shraddha]

Hi all, I'd appreciate some help on the salmon-to-DESeq2 pipeline outlined here. It seems to require a samples.txt file, which I don't have anywhere. I used Salmon to quantify my assembled transcripts (40 x 3 = 120 quant.sf files), and would like to proceed with differential expression analysis.

My datasets consist of 20 samples, 10 of category A and 10 of B. Each category contains 10 samples with two variants; one control and one infected. Also, I'm using a non-model organism plant, so several commonly available files (e.g., for homo sapiens) are not available to me.

So in this case, do I need to create the samples.txt file myself? Alternately, where can I generate/find this file?

Thanks and kind regards

[cpad0112]

I believe so. Open the example samples.txt and create in that format. with R or shell script, you can do it in few minutes.