Hello Etay, After you've submitted your selections to the Table Browser and chosen "sequence" as your output format you will be taken to a menu that has an option for retrieving reverse complemented sequence for minus strand genes. So with these options selected:
clade: Mammal genome: Human assembly: hg19 group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownCanonical filter: transcript 'doesn't match': n/a output format: sequence hitting "get output" should take you to a menu where the last option is: " Reverse complement (get '-' strand sequence)" if this is unchecked you should retrieve sequence that is not reverse complemented. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 6/6/12 2:45 AM, Etay Ziv wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
