[Genome] downloaded exons

[Angie Hinrichs]

Hi Chris,

Here's a small addition to Kayla's explanation.  You might be 
wondering about the extra _0 following the exon number:

> 2.  exon_0_0 is the number of the exon.  You'll note that the next exon
> is labeled "exon_1_0".

-- I was!  I had to look it up in the code.  It is the number of extra 
bases appended to each end of the exon.  In your case (and in most 
cases I think), 0 bases were appended so you're getting just the 
exons.  

It comes from the Table Browser's "Output track as BED" options page:

Create one BED record per:
...
(*) Exons plus [0] bases at each end

Hope that helps,
Angie


On Thu, 6 Mar 2008, Kayla Smith wrote:

> 
> Hello Chris,
> 
> This is best described with an example.  I shall choose the "CITED2" 
> gene on the hg18 assembly.  For your reference, this gene is at this 
> position: chr6:139,735,090-139,737,478.  Please note that this gene is 
> on the reverse strand, which you can see from the <<< arrows on the 
> display of the gene.
> 
> Once I have this gene in view in the Genome Browser, I click on "Tables" 
> to go to the Table Browser.  I use the following settings:
> 
> clade: Vertebrate;  genome: Human; assembly: Mar. 2006
> group: Genes and Gene Prediction Tracks;  track: UCSC Genes;
> table: knownGene; position: chr6:139,735,090-139,737,478
> output format:  BED.
> 
> Click "Get output" and on the next page select the radio button next to 
> "Exons", and click "Get BED".
> 
> Here are the 2 lines of output:
> 
> chr6    139735089    139736782    uc003qip.1_exon_0_0_chr6_139735090_r 
>    0    -
> chr6    139737242    139737478    uc003qip.1_exon_1_0_chr6_139737243_r 
>    0    -
> 
> 
> Looking at: uc003qip.1_exon_0_0_chr6_139735090_r
> 
> Here we have:
> 
> 1.  uc003qip.1 is the name of the UCSC gene
> 2.  exon_0_0 is the number of the exon.  You'll note that the next exon 
> is labeled "exon_1_0".
> 3.  chr6_139735090 is the starting position of that exon
> 4.  r means "reverse strand"
> 
> I hope this information is helpful to you.  Please don't hesitate to 
> contact us again if you require further assistance.
> 
> Kayla Smith
> UCSC Genome Bioinformatics Group
> 
> 
> 
> Chris Zaleski wrote:
> > Greetings,
> > 
> > I have a question about downloaded BED files from the table browser. I've
> > chosen a 'Gene' track, BED output format, and then Exons (from the 2nd
> > page). An example 'name' field looks like the following:
> > 
> > NM_152486_exon_0_0_chr1_850984_f
> > 
> > I understand most, but not all, of the tokens in this string. Could you
> > please explain what all the items represent?
> > 
> > Thanks very much,
> > Chris Zaleski
> > Bioinformatics Team Lead
> > Tenenbaum Lab - SUNY Albany
> > _______________________________________________
> > Genome maillist  -  Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
> 

-- 
angie at soe.ucsc.edu
Software Developer, UCSC CBSE / Genome Bioinformatics Group