HT-Seq Batch

Question

[Nai]

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

[Lila M]

why don't you run it and figure it out?

[Nitin Narwade]

you can try this, it will generate a count matrix for all .sam files in the current folder

./local/bin/htseq-count *.sam ./hg19.gtf >count.mat.tsv

[lieven.sterck]

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)

[Nai]

Thank you...

1. Here I should not call .sam in a variable $i.
2. I have one more query regarding to convert count.mat.tsv to TPM matrix. How can I do that? I have to find eQTL . ....

[Nai]

Thank you Lieven and Nitin! Can you guide me how to convert read count matrix to TPM matrix.

[Nitin Narwade]

This post discussed TPM and other normalized count matrices and also has a link for a code to convert raw count to TPM.