Hi Mbandi, Thank you for contacting the mailing list, and yes, this is the correct place to ask your question. One of our engineers suggests you use psl since it is the native blat format, and not to use fastmap for ests which may have introns in them. In addition, you may download our latest version of BLAT which contains a few bugfixes and may be useful for your purposes. The lastest BLAT is available in compiled form in our downloads: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads. We also suggest you use pslReps and pslCDnsFilter for filtering psl results.
I hope this information is useful and answers your question. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 6/14/2012 1:23 PM, Mbandi S.K wrote: > Dear ALL; > > Firstly, I'm happy to join this mailing list. I do not know if this group > is the right place for my question. Kindly bear with me if my question is > trivial or has been dealt with already. I have recently settled on BLAT v. > 34 for a portion of my project to screen for EST(cDNA) that well aligned > to my reference sequence. However, I find it hard to understand the > effects of -minIdentity and -fastMap on the output. > > I also noticed that just changing the output format, affects the the > reports in the output file. More ESTs are reported in sim4 format than in > psl format. I want to write a parser to calculate coverage, identity etc > in other for me to build a filtering matrix. attached here are two test > files:query.fa and target.fa. I'm aware -fastMap is for DNA-DNA, but just > for test purposes, I ran: > blat target.fa -t=dna query.fa -q=dna -out=psl -minIdentity=100 -fastMap > -dots=1 test.psl > and > blat target.fa -t=dna query.fa -q=dna -out=psl -fastMap -dots=1 test.psl > > However in the first instance; I do not find hits which I expected even > though default -minIdentity is 90 which is less stringent to 100. When > out=sim4 is used, the hits are totally different. Query.fa contains > mutated and unmodified versions of seq1 from target.fa file. > > Has anyone experience strange results like this? Which output is better > from experience? I will appreciate clarity in this regard. > > Many thanks, > > Mbandi S.K > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
