Hello Fahim, We recommend you use pslReps and pslCDnaFilter from the kent source tree to narrow down your results. Here is a previous user question (and our answer) along the same lines as yours: https://lists.soe.ucsc.edu/pipermail/genome/2007-March/012948.html
Here is another that gives an explanation about BLAT scores: https://lists.soe.ucsc.edu/pipermail/genome/2005-August/008231.html Our source downloads are here: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads pslCDnaFilter is available as an executable here (select your preferred platform): http://hgdownload.cse.ucsc.edu/admin/exe/ Hopefully these tools will help you sort through your results. Please contact us again if you have further questions, Best Antonio Coelho UCSC Genome Bioinformatics Group Fahim Md wrote: > Hi > I am using BLAT for mapping sequences of different length ranging from > oligos to a complete gene sequence. For small sequences I am using your > recommendation from http://genome.ucsc.edu/FAQ/FAQblat.html website for > short sequences. As I go towards higher level of annotation for example est > sequences or ensemble gene sequences, I am getting multiple hits(too much to > handle) with default BLAT parameters. > I was wondering if you know of any correpondence between the query sequence > length and the score/identity generated by BLAT(I followed your instruction > to generate score and identity from the psl file). For example, which blat > score is acceptable for sequence length 100 or 1000 or 10000. I am > interested in the best alignment or n-best alignments and not all. > thanks and regards. > Fahim > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
