Conversion error from PSL to bigPsl
Wilson Leung
The bedToBigBed tool reported an error during the conversion of some of
the BLAT alignment results in PSL format to the bigPsl format. I would
appreciate your guidance on the correct way to accomplish this data
conversion so that the results can be visualized in the UCSC track hub.
Attached is a tar gzip archive which contains the test data that can be
used to reproduce the issue. The "test_runner.sh" script within the
archive encapsulates the BLAT search and the data conversion steps that
resulted in the error.
== Kent tools version ==
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
(Last modified: 12-Jul-2016 15:37)
== Steps to reproduce ==
1. Perform translated BLAT search (-q=rnax -t=dnax)
2. Convert PSL to bigPslInput using pslToBigPsl with FASTA and CDS files
3. Convert bigPslInput to bed12+12 format using bedToBigBed
(See test_runner.sh in the package for complete list of parameters)
== Expected result ==
bigPsl file with the translated BLAT alignment results
== Actual result ==
Error reported by bedToBigBed:
Error line 1 of chr1_region.bigPslInput:
BED blocks must span chromStart to chromEnd. BED chromStarts[0] = 2015,
must be 0 so that (chromStart + chromStarts[0]) equals chromStart.
== Comment ==
This conversion error appears only in PSL alignments that are on the
minus strand (i.e. column 15 = "-" in the bigPslInput file).
Please let me know if you have any questions regarding the analysis
steps that resulted in this error or if you require more information.
Thanks for your help.
Sincerely,
Wilson Leung
Elgin Lab
Washington University in St. Louis
Christopher Lee
Hi Wilson,
Thank you for reporting the issue. A fix for this bug will be available in our next software release a couple of weeks from now. Thanks again and we apologize for the inconvenience.
If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.
Christopher Lee
UCSC Genomics Institute
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Christopher Lee
Hi Wilson,
Thank you again for submitting the bug report. We have fixed this
bug in our most recent software release. If you re-download the
pslToBigPsl binary your test script should work.
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
Let us know if you have further problems!
Thanks,
Christopher Lee
UCSC Genomics Institute