[Genome] Using Tables with custom tracks

[Kayla Smith]

Hello Alexandre,

I'll go over with you the steps to get sequence from a list of 
coordinates.

First, you'll want to make a Custom Track.  This can be done using the 
Custom Track tool:

http://genome.cse.ucsc.edu/cgi-bin/hgCustom

You could also get to that link from the Gateway page of any assembly by 
clicking on "add custom tracks".  Here you can paste in the genomic 
coordinates that you're interested in.   Keep in mind that they should 
be in BED format.  For example:

chr22   20100000 20100100
chr22   20100011 20100200	
chr22   20100215 20100400
chr22   20100350 20100500
chr22   20100700 20100800
chr22   20100700 20100900

Once you've submitted that, click on "go to table browser"

At that point you can leave the settings as they are in the table 
browser.  They will default to having your custom track selected.  You 
don't need to paste anything in at this point.  Go to "output format" 
and select "sequence".  Then "get output".  That should do it.

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group



Alexandre Blais wrote:
> Hello UCSC team,
> 
> I am experiencing a problem using Tables with my own custom tracks.
> 
> My goal is to get genomic sequence for a bunch of genomic coordinates.
> 
> I am uploading the coordinates as custom tracks.
> 
> So under "Tables", my approach is to select "sequence output", and
> choose the following:
> 
> Group: Custom tracks
> 
> Track: User track
> 
> Table: ct_UserTrack
> 
>  
> 
> And enter the names of my tracks there.
> 
> When I click on "paste list", I get the following message:
> 
> "Can't start query: describe ct_UserTrack 
> 
> mySQL error 1146: Table 'hg18.ct_UserTrack' doesn't exist"
> 
>  
> 
> What I am doing wrong?
> 
> I double checked to make sure I am looking in the same assembly I
> uploaded the tracks in.
> 
> I can see the entries of my custom tracks just fine, in the browser...
> 
> I am assuming I don't have to intersect or create any filter.
> 
>  
> 
> I tried with various genome assemblies, and I get the same message in
> all cases.
> 
> I am afraid I am doing something completely wrong...
> 
> Thanks much for your help!
> 
>  
> 
> Alex
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome