Hello, I was using pslToBed on some protein psls that I got from BLAT (no header) and I noticed that it does not convert them to bed properly. The resulting bed file will load with hgLoadBed without any issues or complaints (which is dangerous in and of itself) but if you go to upload the bed file as a custom track, it will not work because the coordinates and block sizes are messed up. Here's an example of a psl alignment from BLAT:
504 0 0 0 1 1 11 10637 +- XP_001339893 505 0 505 chr5 74451498 74321062 74333211 12 94,33,12,34,55,66,26,42,51,36,33,22, 0,94,127,139,173,228,294,321,363,414,450,483, 118287,118649,120008,121622,124356,124779,125120,125309,126030,126262,127101,130370, will give the following bed which cannot be loaded as a custom track: chr5 74321062 74333211 XP_001339893 1000 +- 74321062 74333211 0 12 22,33,36,51,42,26,66,55,34,12,33,94, 66,3335,4174,4406,5127,5316,5657,6080,8814,10428,11787,12149, Says: *Error line 1 of custom track: BED chromStarts[i]+chromStart must be less than chromEnd. *I have* *other samples which give different errors such as chromStart + blockStart[lastBlock] + blockSize[lastBlock] != chromEnd (I am paraphrasing the error because I can't find the problematic alignment right now). I'm pretty certain that there's a multiply by 3 issue going on somewhere because the protein is in psl space. Am I doing something wrong? Thanks, Saatvik _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
