My settings screenshot seems to be lost in at least the archive, so for reference the capture is at:
http://traeki.freeshell.org/images/gtf_trial1.png And the key pieces (that I'm aware of) are the settings: group: All Tables table: knownCanonical output format: GTF On Wed, Feb 1, 2012 at 3:12 PM, John Hawkins <[email protected]> wrote: > I'm trying (and failing) to get the UCSC genome browser to output what I > need, and would appreciate guidance. > > My goal is to get essentially the refFlat table data for the > knownCanonical transcripts. > > In other words, I want to get GTF encoded information about transcripts, > with the gene/transcript names flattened into the data, but I only want to > see data for canonical transcripts, not all possible. > > Can this be done directly? If not, any suggestions for how to most simply > approximate it by merging things on my end? > > The settings I've tried look like this: > > > > but this gives me lines like: > > chr1>---hg19_knownCanonical>----exon>---322037>-326938>-0.000000>-------.>------.>------gene_id > "gene9"; transcript_id "tx9";- > > where "gene9" and "tx9" are just iterative line-by-line counters that are > clearly meaningless because they never repeat. Meaning that each exon has a > unique (and numerically matched) "transcript" and "gene" label with no > semantic content. > > And also I don't appear to get strand information. > > In the past I know I've been able to get BED files that contained strand > info and at least grouped exons by transcript, though I don't recall the > settings that got me there... > > Anybody see what I r doin rong, here? > > Thanks, > > -John -- "mFphrrrbm hoAmn rggh, hnllmmgh rnbnrrl." --Demosthenes, "The Early Works" _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
