using blat to align pac-bio reads

[Timms, Andrew]

Hello,

I’m trying to line up a few pac bio reads to the zebrafish genome using blat.

When using the webbased blat I get a result such as (with many more):

  ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
---------------------------------------------------------------------------------------------------
browser details YourSeq         3255   251  7720  8024  92.2%     6   +   59352014  59358576   6563

Which makes a lot of sense, however when I try to do this on by standalone version I end up with lots and lots of smaller hits, the largest having ~1100 matches in a different region.

I’ve tried following the guidelines, https://genome.ucsc.edu/FAQ/FAQblat.html#blat5, but unfortunately that doesn’t help.

Thanks for your time.

Andrew

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[Christopher Lee]

Hi Andrew,

Thank you for your question about replicating web-based Blat on the command-line.

As you noted on the FAQ page, the command-line and web-based versions of Blat
are known to produce slightly different results. Blat was created in order to
align cDNA fragments to the genome, and is not a general purpose aligner. Since
Blat is finding too many hits, you can try filtering the output with the pslReps
or pslCDnaFilter utilities, as the FAQ page mentions:
https://genome.ucsc.edu/FAQ/FAQblat.html#blat5

You can find these utilities on our downloads page. Once on the page select
your machine type and you will see pslReps and pslCDnaFilter:
http://hgdownload.cse.ucsc.edu/admin/exe/

Apart from the help page you've found, here is a previously answered mailing list
question that goes into detail on setting up gfClient/gfServer in order to replicate
web-based Blat output that you may be interested in:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/tntQgkf_NTA/ufmiEB17IgAJ

For more information on Blat, see the Blat Specification and User Guide:
https://genome.ucsc.edu/goldenPath/help/blatSpec.html

For non-UCSC discussions about aligning PacBio reads, including recommendations
for software other than Blat , see the following:
https://www.biostars.org/p/116696/
http://seqanswers.com/forums/showthread.php?p=152941#post152941
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-238

Thank you again for your inquiry and using the UCSC Genome Browser.
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.

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