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!
-
-
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.
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM
Comment