Here is an example that just counts the number of alignments
on each chromosome for the positive strand.
cat output.psl | gawk '{if ($9 = "+") print $14}' | uniq -c
similary for the negative strand.
cat output.psl | gawk '{if ($9 = "-") print $14}' | uniq -c
Yes, you are right that it never outputs more than 16 per strand
per chrom. This is a built-in limit of BLAT.
-Galt
On 05/18/11 11:14, Tyler Garvin wrote:
> For example here is a simple run without changing many parameters:
>
> blat -maxIntron=3000 -noHead database consensus.fa output.psl
>
> my database is a path to .nib files for each chromosome that was originally
> from the hg18 chromFa file:
> home/chr10.nib
> home/chr11.nib
> home/chr12.nib
> home/chr13.nib
> home/chr14.nib
> home/chr15.nib
> home/chr16.nib
> home/chr17.nib
> home/chr18.nib
> home/chr19.nib
> home/chr1.nib
> home/chr20.nib
> home/chr21.nib
> home/chr22.nib
> home/chr2.nib
> home/chr3.nib
> home/chr4.nib
> home/chr5.nib
> home/chr6.nib
> home/chr7.nib
> home/chr8.nib
> home/chr9.nib
> home/chrX.nib
> home/chrY.nib
>
> The output gives the following number of sequence results for each chromosome:
>
> chr1 count = 32
> chr2 count = 32
> chr3 count = 32
> chr4 count = 32
> chr5 count = 32
> chr6 count = 32
> chr7 count = 32
> chr8 count = 32
> chr9 count = 32
> chr10 count = 32
> chr11 count = 32
> chr12 count = 32
> chr13 count = 32
> chr14 count = 32
> chr15 count = 32
> chr16 count = 32
> chr17 count = 32
> chr18 count = 32
> chr19 count = 32
> chr20 count = 32
> chr21 count = 32
> chr22 count = 32
> chrX count = 32
> chrY count = 17
>
> I have tried using the original .fa files in my database path rather than the
> .nib files and I get the same results. I've also run each chromosome
> separately and also get the same results. I have also already tried setting
> minScore=0 with no real change in results. I still have no idea why blat
> limits my results to 32 per database (chromosome).
>
>
> ----- Original Message -----
> From: Galt Barber <[email protected]>
> Date: Wednesday, May 18, 2011 11:00 am
> Subject: Re: [Genome] Quick Blat Question
> To: Tyler Garvin <[email protected]>
> Cc: [email protected]
>
>> It would be helpful if you provided an example.
>>
>> http://hgwdev.cse.ucsc.edu/FAQ/FAQblat.html#blat5
>>
>> Try setting minScore=0.
>>
>> -Galt
>>
>> On 05/18/11 10:19, Tyler Garvin wrote:
>>> Hi all,
>>>
>>> I recently downloaded blat and and have been using it from my
>> computer (rather than using web based blat). I have been trying to
>> use blat to gather my own SVA data using the SVA consensus sequence
>> from RepBase. The output from blat, though, has never give me more
>> than 32 results per chromosome. I even used a number of small
>> random sequences for my query and I still got a max of 32 results
>> per chromosome.
>>> I tried installing blat from a number of different places in the
>> hope that I simply had a corrupted blat executable but every
>> download gives me the exact same results. I have also played with
>> a number of parameters and none of them seem to change my results
>> much. My database is a text file that has paths to .nib files for
>> each chromosome of the human genome.
>>> If anyone knows why this may be happening or how I should fix it I
>> would really appreciate it.
>>> Thanks
>>> T
>>> _______________________________________________
>>> Genome maillist - [email protected]
>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
