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Old 05-17-2015, 04:38 AM   #6
Location: London

Join Date: Jan 2015
Posts: 10

Originally Posted by GenoMax View Post
Are you trying to look at a specific region of the chromosome? If so you can extract just the reads aligning in that region using samtools (check out the view command). Then use original (or modified) GTF file with this extracted region in the new BAM file.
Ah!! This is what I needed to know!! Yes, I am trying to align my reads to a specific part of the chromosome due to computational limitations..

Thanks so much for your help!
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