UCSC Blat Result Problem
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:
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
SRST2
written by anjalivasudevan98 •
-
Problem with file location address in HISAT2
written by Yoosef •
-
deepTools : No module named cycler
written by mbk0asis
-
Why can't import Biopython module when I run my scripts located in /usr/lib/cgi-bin?
written by lhernanj •
-
Why can't import Biopython module when I run my scripts located in /usr/lib/cgi-bin?
written by lhernanj •
-
BLAT installation *** No rule to make target '../lib//jkweb.a', needed by 'blat'
written by marongiu.luigi
-
troubleshooting: error on run of kissplice2refgenome
written by celine •
-
How do I compile Quake (error correction of Miseq reads) in Ubuntu?
written by fhsantanna
-
Seqlogo and Homer
written by fire_water
-
Where To Get A List Of Species?
written by michaelfaraday •
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 comis a common host and change the links in your post.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=0etc.). Unfortunately, results of local blast are not same with web results.Also, I updated image sources.
Thanks ...
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
chr17:7669609-7677594and ended up with a 1100+ hits with localblatthe suggested options (-stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0) withhg38. Same sequence on UCSC web blat geneated ~217 hits.