Does Blat can take multiple reference sequence in one command line

[jjjscuedu]

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

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

Commonly, I will do like this:

faToNib in.fa out.nib
blat out.nib query.fasta output.psl

However, the in.fa file can only have one sequence

How can i do that for many reference sequence?

Thanks!

Jingjing

[GenoMax]

You should be able to concatenate multiple sequences together into a single file and use that as the reference.

[jjjscuedu]

if in.fa contains multiple sequence file, there will be an error message like this:

faToNib only works on fa files containing a single sequence.

[GenoMax]

if in.fa contains multiple sequence file, there will be an error message like this:

faToNib only works on fa files containing a single sequence.

You could use the multiple fasta file as is, without converting it to the nib format as your reference. I have not tried "a list these files one file name per line" option, but it seems to be there.

---------------------------------------------------------
blat - Standalone BLAT 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.