psl does not store sequences. pslx (which is only used rarely) will store the sequence of the query and the target (for aligning blocks only concatenated together).
There is no sam output option for BLAT at this time. -Galt Ar 6/4/2010 8:47 AM, scríobh Drewry, David G.,III (NSTD): > Is there a flag for reporting blat outputs in SAM format or have you written > a script to do this. SAMtools currently contains a psl to SAM converter, however, the sequences are not preserved. > > Thanks, > David > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
