I am attempting to count the number of reads of each isoform of the Rt-GEF gene in Drosophila across multiple sam files. My sam files are currently formatted so that reads are listed by coordinates on chromosomes, such as
VH00562:14:AAANWG5HV:1:1101:26828:1568 1:N:0:ACTAAGAT+GCGGTTGT 99 chrX 5075295 42 50= = 5075328 83 CTTTTAAAAAAAAATCAATACCTTACTTAAACTAACTATGCAAAAAATCG CCCCC;CCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCC NM:i:0 AM:i:42 .
However, I am trying to get my data in a format that converts these to the isoform expressed by the read, ideally using a FlyBase ID so that I can count them. Is there any way to change the files to a more readable format? Thanks!