python importing featureCounts to automate multiple files
Hello I'm trying to use featureCounts for multiple files using python script
but python doesn't seem to be able to load featureCounts feature.
My python script is as below.
import os import sys number=['ss','sss',ssss','ssss'] for a in number: os.system("featureCounts -a /home/biguser/systems_biology_2021/TA/gtf/gencode.v34.gtf -p -o /home/biguser/xxxxxxxxxxxx/xxxxxxxxxxx/organizedF/feaC/%s/%s_feaCon.txt /home/biguser/xxxxxxx/xxxxxxxx/organizedF/mappedControl/%s/%s_Aligned.sortedByCoord.out.bam -T 4"%(a,a,a,a))
And the result.
[[email protected] finalP]$ python pyfeaCon.py sh: featureCounts: command not found sh: featureCounts: command not found sh: featureCounts: command not found sh: featureCounts: command not found
I'm pretty new to these stuff, so I was wondering if i could get any help
P.S How do I create a new line in this thing? Even if I 'enter' it just stays in a paragraph.
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