BLAT does appear anything in the results but blat worked.

Question

[margxenscienculo]

Hi everyone. I am trying to make a blat but it is working anyway. I changed from .fa to .2bit format, neither it work. I only try to get sequences similarity with mature(mirbase). I wonder if it could be some specific library, or if blat have to connect with other tool or other stuff.

blat software: http://genome.ucsc.edu/goldenPath/help/blatSpec.html

Thanks in advance.

 ./blat mature_mirbase.fa  candidate_mirna.fa -q=rna -stepSize=2 -tileSize=8 out.blast8
Loaded 781222 letters in 35828 sequences
Searched 4313 bases in 205 sequences

But I only get a empty file results.

sLayout version 3

match    mis-     rep.     N's    Q gap    Q gap    T gap    T gap    strand    Q            Q       Q        Q      T            T       T        T      block    blockSizes     qStarts     tStarts
         match    match           count    bases    count    bases              name         size    start    end    name         size    start    end    count
---------------------------------------------------------------------------------------------------------------------------------------------------------------

[Vivek]

Are your queries atleast 20 bases long?

[margxenscienculo]

My queries are several length. Why? do you think that Blat does not work with smaller sizes?

[Vivek]

Minimum query size for blat is 20bp.

[Lorena Pantano]

I think this is only if you don't change tilesize, stepsize, and the rest of parameters. I am getting 13 nt match changing those to very low values. Make sure the database is DNA (not Us).

Answer 1

[Lorena Pantano]

Hi,

You can try to add -minMatches=1 -minScore=10 -minIdentity=50

Al well, you can generate a test data with some mature miRNA in mirbase.fa, to check is giving you some hits, and as well, modifying this example with some mis-matches or doing only that half of the sequence is identical to the miRNA but not the rest. Just to tune your parameters with the positive hits you know should be there.

Hope this helps

[margxenscienculo]

Thanks L. Pantano. Only I felt shocked that the program did not work. Yes, it gave me some hits. Now, I have to tune.

Moltes gracies!

Answer 2

[Siva]

Have you looked at this?

Using Blat for short sequences with maximum sensitivity

[margxenscienculo]

Thanks! Your message and the other user will able to help me.