Hi Ann, One of our developers writes: "Xeno RefSeqs are aligned using protein-translated BLAT, which is able to align farther evolutionary distances that DNA BLAT. It also uses repeat masking, which is not done for the native RefSeq alignments.
The blat parameters are blat -noHead -repeats=lower -q=rnax -t=dnax -mask=lower" I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 4/4/11 7:21 PM, Ann Loraine wrote: > Hello, > > I have a question about how you generate the "Other RefSeq" tracks. > > What parameters do you provide to blat in creating these tracks? > > I read this description in the Methods section: > > "The RNAs were aligned against the [species] genome using blat; those with > an alignment of less than 15% were discarded. When a single RNA aligned in > multiple places, the alignment having the highest base identity was > identified. Only alignments having a base identity level within 0.5% of the > best and at least 25% base identity with the genomic sequence were kept." > > This describes the how the post-alignment filtering works but doesn't > provide the parameters used for the initial blat run. > > What parameters do you supply to blat in order to create the initial > alignments? > > Sincerely, > > Ann Loraine > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
