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Hello, I am working with a BAM file which compares a differentiated cell genome to that of a reference sequence genome. To be more specific, I am comparing differentiated T-cell receptor to germ line VDJ regions. Is there any way to output the VDJ region of the differentiated sample as a FASTA file so I can identify it on BLAST? Thanks!
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If your .bam file was made by aligning reads to a genome, then it's got the chromosome and position of every read that aligned. So you can filter the bam by position to get only the regions you want. SAMTools view can do this, there are probably ways in other software suits, like Picard and GATK.
After that, you've got to do something with teh .bam, and that depends a lot on what exactly you are trying to do with your data.
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