Does standalone Blat can take multiple chromosome in one command line, find matches?

[ketan_bnf]

Hello All,


I have successfully used blat executable on my system, but the problem is i am able to take only one chromosome as reference database against query sequences.

Now i want to take multiple chromosome as reference database in one command line and find query allignment.


How can i do that?

[jjjscuedu]

Did you find the solution for this problem?

[zhiqiang]

It will of course work according to its help documentation.

blat - Standalone BLAT v. 34 fast sequence search command line tool
usage:
blat database query [-ooc=11.ooc] output.psl
where:
database and query are each either a .fa , .nib or .2bit file,
or a list these files one file name per line.