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 -- Ann Loraine Associate Professor Dept. of Bioinformatics and Genomics, UNCC North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 www.transvar.org _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
