UCSC Blat Result Problem

Question

[selam]

Hi everyone! I installed local BLAT on my OS named Ubuntu and I run it. However, I'm wondering that why the result of the my local blast is not same the web result (https://genome.ucsc.edu/cgi-bin/hgBlat). I'm using same database and query sequence/file but the result doesn't look like web result.

*How can I get same result with my local blat system like web version ? *

Thanks ..

Web Result:

My Local Result:

[GenoMax]

Have you seen this link from UCSC to make your web blat look similar to the command line version?

I also suggest that you post your images to a more common free image hosting site imgbb dot com is a common host and change the links in your post.

[selam]

Hi,
yes, I've seen it but I installed binary version of ucsc blat not gfserver and tried many filters like on the page (stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 etc.). Unfortunately, results of local blast are not same with web results.

Also, I updated image sources.
Thanks ...

[GenoMax]

Are you referring to the results containing only one hit locally where as there are multiple on the web? Additional hits on the web have low scores and are for much smaller regions. You are blat'ing a human sequence against the human genome, right?

Edit: Tried sequence from interval chr17:7669609-7677594 and ended up with a 1100+ hits with local blat the suggested options (-stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0) with hg38. Same sequence on UCSC web blat geneated ~217 hits.