Hi, Jiping!
If you read the -maxGap description it says
-maxGap=N sets the size of maximum gap between tiles in a clump.
Usually set from 0 to 3. Default is 2.
Only relevent for minMatch > 1.
-minMatch=N sets the number of tile matches. Usually set from 2 to 4
Default is 2 for nucleotide, 1 for protein.
So maxGap here is talking about tolerating a small insertion or deletion
between the high-scoring pairs (default minMatch=2). After finding
an HSP, it uses other methods including dynamic programming to expand
the alignment around the HSP. Finally blat chains the "exons" or
aligning blocks together across a single query to produce a psl record
with "linked-features". Exon-ends (dna only) may be adjusted slightly
to fit RNA-splicing rules.
So increasing maxGap might increase the sensitivity of BLAT
so that it is able to find some more alignments, but it does not
say anything about controlling gaps in the final full psl alignment.
You can try using -fastMap
-fastMap Run for fast DNA/DNA remapping - not allowing introns,
requiring high %ID
You can also try using the -out=blast8 format,
because this returns only "exons" without chaining.
You might try setting -maxIntron=0, but I have not tried this.
-maxIntron=N Sets maximum intron size. Default is 750000
Finally I recommend to everyone to use pslCDnaFilter or pslReps
to filter your psls made by BLAT. It often gives better control
over the results than tweaking blat parameters.
And if you are trying to do short reads, remember that
there are now many fine free short-read aligners like MAQ and Bowtie.
-Galt
Ji-Ping Wang wrote:
> Hi,
>
> Can anyone help on how to generate local alignment without gaps using
> blat? I try to use commands as follows:
>
> blat seq1.fa seq2.fa -minIdentity=100 -maxGap=0 out.psl
>
> always generate alignment with gaps.
>
> Thanks.
>
> Jiping wang
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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