BLAT search in only 1 chromosome

[Hector Soemedi]

Hi - is it possible to use BLAT search to obtain matches in 1 chromosome only?

thanks,

HS

[Gerardo Perez]

Hello,

Thank you for your interest in the UCSC Genome Browser and for sending your inquiry

The only way to BLAT search matches in 1 chromosome would be to run standalone blat using the command line. You would use the /path/file.2bit:seqid:start-end setting where seqid would be the chromosome. Here is how you can run standalone blat using this setting on hg38 for chromosome 20:

blat -stepSize=5 -repMatch=2253 -minScore=20 -minIdentity=0 hg38.2bit:chr20 query output.psl

More information on standalone blat can be found in the Blat Suite Program Specifications and User Guide: https://genome.ucsc.edu/goldenpath/help/blatSpec.html

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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