UCSC canonical transcripts with identifiers in GTF

[traeki]

I'm trying (and failing) to get the UCSC table viewer 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