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Putnam-Lab / Lab_Management

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StringTie count matrices from GTF files: update to prepDE.py script! #87

Closed daniellembecker closed 3 months ago

daniellembecker commented 3 months ago

Recently found out that there is a new prepDE.py script when you need to generate gene and transcript count matrices from a set of GTF files produced by StringTie:

Moving forward, use the prepDE.py3 script , which you can load into your directory using "wget https://raw.githubusercontent.com/gpertea/stringtie/master/prepDE.py3".

I also added it to our shared scripts directory in the Andromeda putnamlab folder: cd /data/putnamlab/shared/scripts/

JillAshey commented 3 months ago

what's the difference between the two?

daniellembecker commented 3 months ago

its a syntax difference between running python2 and python3, some differences were for the print statements (needed to have parentheses around them) and other syntax changes when using the updated Python/3.9.6-GCCcore-11.2.0 module

hputnam commented 3 months ago

You should be able to use either one with the same results. One is based on python version 3 and named as such. In my understanding, this should not cause differences in the count matrix itself

daniellembecker commented 3 months ago

sounds good, I was getting syntax errors consistently in my slurm outputs and couldn't run the original prepDE.py script with the updated module but yes I don't think it would cause difference in the count matrix