Question: Problems uploading custom track to UCSC Genome Browser
0
gravatar for rs
11 months ago by
rs40
United Kingdom
rs40 wrote:

Hello,

I have a GTF file that I would like to visualize in the UCSC genome browser. When I upload it, it centers the browser window to where I've asked it to on the track line but the track itself is not displayed in the browser. It doesn't show up below the browser in the list of tracks either. I have tried clearing my cache, resetting the browser (like in the official troubleshooting guide), tried using another browser...

Any help would be greatly appreciated! This is what the start of the file looks like:

browser position chr1:12228-12612
track name="introns" description="Intron coordinates" visibility="2"
chr1    havana  transcript  12228   12612   .   +   .   gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
chr1    havana  transcript  12722   12974   .   +   .   gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
ucsc genome browser • 450 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by rs40

genomax, thanks for your help with formatting the example!

ADD REPLYlink written 11 months ago by rs40

It looks fine but you can try to upload just the file without first two lines and add them manually in Edit custom track (when you click on the track after uploading it) in Edit configuration. Also try visibility=full and can specify graphType

ADD REPLYlink written 11 months ago by marina.v.yurieva480

Thanks Marina! I tried that (removing the broswer and track lines, changing the visibility setting, explicitly setting track type) but it's still not working. It's really strange, I have done this before using other BED files and GTF files and this time it just won't work.

ADD REPLYlink written 11 months ago by rs40

Does it recognize it as a bed file? (when you upload it go to Manage custom tracks, it should list your file and show file type, number of items in the table. If it doesn't show that file type is "gtf" maybe there is something wrong with formatting. You can check it with vim for tabs etc. It can also be something stupid like encoding issue, you can do dos2unix to change it.

ADD REPLYlink written 11 months ago by marina.v.yurieva480

Still no luck. But it does look like it may be a formatting issue: when I upload it, it doesn't display the "Items" column, as if there were no items.

ADD REPLYlink written 11 months ago by rs40

I think that is happening because your ID's are not UCSC.

ADD REPLYlink written 11 months ago by genomax70k

UCSC definitely takes Ensembl IDs but I don't remember if there should be ENSGXXXX.X or it doesn't need ".X" at the end..

ADD REPLYlink written 11 months ago by marina.v.yurieva480

I have tried coverting to BED or removing the last column of the GTF but that doesn't seem to help. Then I figured I'd just used the Ensembl Genome Browser instead. Alas the items are not showing up on Ensembl either.

ADD REPLYlink written 11 months ago by rs40

But it does recognize it as a GTF (or as a bed, if I reformat it as a BED).

ADD REPLYlink written 11 months ago by rs40

Just to say that I have solved the problem by using the Ensembl Genome Browser instead (which isn't half as convenient but maybe I'm just not used to it).

ADD REPLYlink written 11 months ago by rs40
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