blat

[Yuan Jian]

hello,

I have downloaded blat standalone version. i can blat 20bp sequence at UCSC genome web browser, but in standalone version, i get no answer. how can i query a sequence of size 20 bp in standalone version?

thanks

Yu

[Matthew Speir]

Hi Yu,

Thank you for your question about using command line BLAT. Unfortunately, BLAT was not designed to find short sequences and the default parameters for the program are not sensitive enough to find these short sequences. However, the web-based BLAT parameters are tuned to potentially find these matches. You can more information on tuning the command line BLAT parameters to find your 20bp sequences here: http://genome.ucsc.edu/FAQ/FAQblat.html#blat8. I would also recommend looking into other command line programs designed to align short sequences, such as Bowtie.

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.

Matthew Speir
UCSC Genome Bioinformatics Group

--