Hi, Saatvik! There was a problem with pslToBed for translated-PSLs. You can expect to see the fix in release v244.
Thank you very much for reporting the issue! -Galt On 11/12/10 19:24, Saatvik Agarwal wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
