wow thanks! it solve the problem
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maxdlf12 •
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.
[biguser@xxxx-master 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
Thanks.
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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Ram
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maxdlf12 •
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maxdlf12 •
1 answer
Glad it helped! A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work. This will help future users that might find this post find the right answer.
Oh Cool. Done!
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