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Old 05-17-2015, 04:15 AM   #5
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077

I am not sure why you are trying to recreate the index files since the bundle contains BowtieIndex and Bowtie2Index, which already have the index files.

GTF files define features in the genome and if you want to add additional ones as long as you stick to the correct format you should not need to mess with the reference or the index files.

If you make any changes to the reference itself (add/delete, even a base) then you will need to recreate the index files and edit GTF file as well since you will have effectively changed co-ordinates of the original genome reference.

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.
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