Hello. I need to re-construct the pairwise alignments (transcript vs genome) for some of your reference sets. Specifically, I'm looking to create an entry something like this: "NM_001160175.1 1-72,73-222,223-340,341-419,420-2067 chr8:18067618-18067689,18068702-18068851,18074386-18074503,18076920-18076998,18079551-1808198:+" for a given set of transcripts. For RefSeq, I was able to parse this information out of refSeqAli.txt. However, I cannot find a corresponding file for your very nice set of entries in the UCSC Known Genes track. The knownGene.txt table contains only the genomic coordinates. Given that the sum of the exon blocks in knownGene.txt does not always match the sequence length in knownGeneMrna.txt, can you tell me how to reconstruct the transcript segment coordinates for the pairwise alignment? Thanks!
Sara Grimm, PhD Lineberger Comprehensive Cancer Center UNC - Chapel Hill _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
