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
