I'm interested in getting a fasta format file for the known genes (limited to canonical) in the hg19 index--I'm using this to then build a custom index for use with bowtie. I've spent some time reading through the archive and found this useful exchange:
https://lists.soe.ucsc.edu/pipermail/genome/2012-February/028372.html from which I learned this non-intuitive useful bit of information: 6. In the "hg19.knownCanonical based filters" section, set the following on the transcript line: transcript doesn't match n/aWhat I'm finding somewhat bothersome is that when I choose sequence output I then get the output in reverse complement form (using both the mrna or the genome option). I can write a script to undo this, but it seems like there should be an output option that does not generate the reverse complement for all of the minus strand genes. Thanks for your help, Etay _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
