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Old 04-06-2018, 07:59 AM   #1
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Default Extracting specific gene regions from BAM file using GTF

I have pooled population data in BAM format for two populations that should have local adaptations. I have identified gene regions with signatures of selection (Fst).

I now wanted to directly compare the exon sequences of these two populations for my list of genes. Since my data is mapped to the whole genome, I was looking for an easier way to pull sequences from genes on different chromosomes. In my mind I would provide the Gene ID, and using the exon range from the GTF file, it would extract the region of the BAM File. If I could then get a consensus sequence saved to a text file of just the exons for that gene, I could continue.

Again, I have the mapped BAM file and the GTF file. I see some people mention converting to a BED file? Is there also a way to reduce that BED file to just my genes of interest or should I do each seperately (If I have say only 20 genes of interest at the moment) If I can get a consensus sequence, I wanted to use blast to translate and compare possible amino acid changes between these two groups.
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bam, consensus extraction, exon, gene extraction

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