Question: Tuning local blat to perform more like UCSC's version
0
gravatar for dchen71
3.1 years ago by
dchen710
dchen710 wrote:

I am trying to find where the 20bp probes I have, lie on the mouse genome. I am trying to tune the parameters to try to match the results that I get when I search it on UCSC. I am hoping someone has some hints into tuning blat.

For reference I am using the following commands for my current results:

gfServer start -tileSize=11 -minMatch=1 -maxGap=2 localhost 3000 Index/mm10.2bit
gfClient localhost 3000 ../mouse Output/test.fa Output/test.psl -t=dna -q=dna -minScore=10
blat • 884 views
ADD COMMENTlink modified 3.1 years ago by mastal5112.0k • written 3.1 years ago by dchen710
1
gravatar for mastal511
3.1 years ago by
mastal5112.0k
mastal5112.0k wrote:

Have you seen

Replicating web-based Blat parameters in command-line version

on the UCSC FAQ pages?

ADD COMMENTlink written 3.1 years ago by mastal5112.0k

I missed that topic but unfortunately, it still gives me a slightly different answer. Hadn't though of trying to use -minIdentity so useful all the same.

ADD REPLYlink written 3.1 years ago by dchen710
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 893 users visited in the last hour