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Hi all, and thanks for taking time to read this, with apologies if an answer already exists – I wasn't able to find it.
I was wondering if anyone knows of a tool that can extract the total number of introns, their length, and the number of reads spanning each putative intron (coverage), given only a BAM file (no known junctions file, no unmapped (raw) reads, only BAM with non-spliced reads removed, and a reference sequence). Basically, I'm trying to find a way to export what IGV draws in the junctions track (or in sashimi plot) based on the data in a BAM file, back to a table format which might look something like this:
…and so on for all putative introns in a given BAM file. Basically, I'd just like to do the brief summarization, as described above. I suspect that this can be done by operating on POS and CIGAR fields, but I have an uneasy feeling that this, in addition to noob, belongs into warm water-inventing territory, which I'd like to avoid if the tool for the job already exists. Therefore, I'd really appreciate your inputs on this matter. Thanks in advance.
I was wondering if anyone knows of a tool that can extract the total number of introns, their length, and the number of reads spanning each putative intron (coverage), given only a BAM file (no known junctions file, no unmapped (raw) reads, only BAM with non-spliced reads removed, and a reference sequence). Basically, I'm trying to find a way to export what IGV draws in the junctions track (or in sashimi plot) based on the data in a BAM file, back to a table format which might look something like this:
Code:
Intron FirstBase LastBase Strand Coverage 1 1000 2000 + 67 2 5800 5600 - 22