Troubleshooting with Deseq2

Hi, I am trying to run DESeq2 on 11 featureCounts file, following this tutorial:

The problem is in the Deseq2 result file, I found out the p-value column are not in descending order, which will influence the p-value histogram result. Any suggestion on how to solve this? Thanks

Hi @H_nh_Le

seems to me that the output is sorted on adjusted p-values (column 4), which is actually what you should look at.

If you really want to focus on raw p-values instead, then there’s the Sort data in ascending or descending order tool. Use its “General numeric sort” flavor on column 3 and it should give you the output you want.


Thank you, I will sort the data before HISAT2 then.