diffSplice files are empty

[ghofrankothoum]

Command: python3 flair-2.0.0/flair.py diffSplice -q quantify.tsv -i all.isoforms.bed -o final_diff -of

How did you install Flair?

2. docker pull brookslab/flair:latest

What happened? diffsplice output files are empty except for the header

**What else do we need to know?**
I had to split the input by chromosome for the collapse command. for flair quantify and diffSplice, I merged (using cat) all of the individual bed and fasta files from collapse.

[Jeltje]

This means it found no differentially expressed isoforms. Have a look at your input count matrix to see if this makes sense. You'll need to see substantial differences between group averages.