Hello, BLAT does provide statstics about insertions/deletions/mismatches. The larger question about how to apply these results with respect to the entire genome is more complicated. It might be a good idea to align all of the sequences (long and short) to the genomic, load as custom tracks, and examine the results in the context of the other annotation in the region (variation, gene preditions, mRNA data). Be aware that there are some limits on how short sequences can be if aligned with BLAT. Sequences from Illumina are right around the lower length threshold. See the BLAT documentation here : http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign
BLAST was not designed to do genomic alignments, but it is used by some groups, and most users will develop tools that involve some complicated post-processing of the alignments to merge HSPs and recalculate statistics, given that evalue is not particularity useful for this type of analysis. Masking would be important if you use BLAST to avoid producing copious amounts of non-specific output. However, evaluating both tools on the same test set will help you to decide which is better for your experiment. Hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Mera Vigyan" <[email protected]> wrote: > From: "Mera Vigyan" <[email protected]> > To: [email protected] > Sent: Friday, August 28, 2009 10:24:01 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] working with long and short reads > > good morning, > > i have a query : > > suppose we are having longer read sequences from Sanger technology and > also > short reads from Illumina from > the same species. > If we run BLAT or BLAST by using the set of long reads as a database > and the > set of short reads as query sequences. > >From this alignment, can we deduce information about insertions, > deletions > in the species. > > thanks > Mera > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
