HT-Seq Batch
Will this shell script for batch ..Related HTSeq-count. will it create separate file for each sample or merge count file. Kindly interpret the scrpt also. Because I am new in batch scripting.
for i in *.sam
do
echo $i
./local/bin/htseq-count $i ./hg19.gtf > $i.count
done
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updated
by
Nitin Narwade
•
written
by
Nai •
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written
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Nai •
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why don't you run it and figure it out?
you can try this, it will generate a count matrix for all .sam files in the current folder
Thank you...
Thank you Lieven and Nitin! Can you guide me how to convert read count matrix to TPM matrix.
This post discussed TPM and other normalized count matrices and also has a link for a code to convert raw count to TPM.
the script you show here will create one count file per input sam file (so no merged output, see Nitin Narwade comment to achieve that merged kind of output)