[Genome] "_dupX" names for transcript ID duplicates on same chromosomes

Angie Hinrichs angie at soe.ucsc.edu
Tue Jun 12 10:37:28 PDT 2007 

Hi Micha,

There is nothing special about the assignment of the _dup suffixes -- 
the Table Browser simply assigns them in the order of retrieval from a 
database query.  If it has already written GTF for a given ID, and 
then gets another element with the same ID, it adds the suffix for 
uniquification as b0b said.  There is no consideration of the quality 
of the items, and it is not stable.  

In case this part of your original question hasn't been addressed 
already -- in order to join with gbCdnaInfo to get the CDS, simply 
chop off the _dup suffix.  The CDS info is a property of the mRNA 
sequence from GenBank, and applies to all genomic alignments of that 
sequence.

The UCSC Genes track does use stable accessions (uc00*.version)... 
no guarantees that it will cover all of the GenBank sequences you are 
working with, but it does have the advantage of stability.  The 
GenBank tracks are particularly un-"stable" because they are 
regenerated regularly (mRNAs nightly, ESTs weekly) so that we can keep 
up with additions and changes in GenBank.  

Angie


On Tue, 12 Jun 2007, Micha Sammeth wrote:

> Hi Robert,
> 
> is there something known about the order that the TB assigns 
> "transcript_id", "transcript_id_dup1", "transcript_id_dup2", ... to 
> transcripts that align multiple times? Is it according to alignment 
> quality (match% or query mismatches or ...?) or according to the genomic 
> order of the transcripts (which one?)? How ties are broken? Is the 
> process stable, ie, are the dupX suffixes the same across different 
> exports from the TB, different genome versions, future Genbank imports?
> 
> Thank you!! micha.
> 
> En/na Robert Kuhn ha escrit:
> > Hello, again, Micha,
> >
> > As you suspect, the transcript_id field is generated dynamically by 
> > the Table Browser as a result of your choice of GTF for output.  On 
> > the following page in our FAQ:
> >
> >   http://genome.ucsc.edu/FAQ/FAQformat#format4
> >
> > that field is defined as
> >
> > "transcript_id value - A globally unique identifier for the predicted 
> > transcript"
> >
> > so it is necessary for the TB to distinguish the two AK130020 transcripts.
> >
> > If this does not fully resolve the issue, please let us know.
> >
> > thanks,
> > 			--b0b kuhn
> >
> >
> >
> >   
> >> From gmicha at gmail.com  Tue Jun 12 02:45:30 2007
> >> To: Robert Kuhn <kuhn at soe.ucsc.edu>
> >> CC: genome at soe.ucsc.edu
> >> Subject: Re: [Genome] "_dupX" names for transcript ID duplicates on same chromosomes
> >>
> >> Hi Robert,
> >>
> >> the following is a grep on a file I downloaded from the table browser 
> >> (mRNA track, hg17, GTF export). So, does the table browser somehow 
> >> dynamically generate these _dup names for multiple alignments on the 
> >> same chromosome?
> >>
> >> Best, micha.
> >>
> >> $ grep AK130020 human_hg17_mRNA_fromUCSC.gtf
> >> chr1    hg17_all_mrna   exon    16385779        16385842        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020";
> >> chr1    hg17_all_mrna   exon    16452373        16452436        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020";
> >> chr1    hg17_all_mrna   exon    16452437        16452447        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020";
> >> chr1    hg17_all_mrna   exon    16452451        16452453        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020";
> >> chr1    hg17_all_mrna   exon    16452454        16452559        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020";
> >> chr1    hg17_all_mrna   exon    17065218        17066019        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020";
> >> chr1    hg17_all_mrna   exon    17067288        17067965        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020_dup1";
> >> chr1    hg17_all_mrna   exon    17068055        17068101        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020_dup1";
> >> chr1    hg17_all_mrna   exon    17068187        17068297        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020_dup1";
> >> chr1    hg17_all_mrna   exon    17068821        17068976        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020_dup1";
> >> chr1    hg17_all_mrna   exon    17071812        17071943        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020_dup1";
> >> chr1    hg17_all_mrna   exon    17072047        17072113        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020_dup1";
> >> chr1    hg17_all_mrna   exon    17072201        17072648        
> >> 0.000000-.gene_i
> >> d "AK130020"; transcript_id "AK130020_dup1";
> >>
> >>
> >> En/na Robert Kuhn ha escrit:
> >>     
> >>> hello, micha,
> >>>
> >>> I'm not sure I understand where you are seeing the "_dup" part of
> >>> transcript_ids.  The chr1_mrna table does have two entries for the
> >>> accession you mention.  
> >>>
> >>> One of these is definitely a better alignment than the other.  Type 
> >>> AK130020 into the position box of the browser and then click on one of 
> >>> them.  Then expand your position window to chr1:16513000-17200000.  
> >>> Both transcripts should be highlighted in the Human Mrna track.  I 
> >>> know that does not address your bulk processing issues, but I thought 
> >>> I'd mention it.
> >>>
> >>> Please let me know where exactly you are seeing the "_dupX"
> >>> notation and I will try to track it down.  By the way, it is
> >>> not uncommon for mrnas to align in more than one location.  the
> >>> existence of segmental duplications virtually guarantees it.
> >>>
> >>> best wishes,
> >>>
> >>> 			--b0b kuhn
> >>>
> >>>   
> >>>       
> >>>> From genome-bounces at soe.ucsc.edu  Mon Jun 11 15:48:27 2007
> >>>> Cc: genome at soe.ucsc.edu, Micha Sammeth <micha at sammeth.net>
> >>>> Subject: [Genome] "_dupX" names for transcript ID duplicates on same
> >>>> 	chromosomes
> >>>>
> >>>> Hello again,
> >>>>
> >>>> thank you, Robert for the explanation on the ESTs, I got it clear now.
> >>>>
> >>>> I have another little problem, hopefully the last one for this project: 
> >>>> when I download the (hg17) mRNA track, I get conveniently unique 
> >>>> transcript_id tags - at least on a chromosome level, which is enough 
> >>>> (e.g., "AK130020" and "AK130020_dup1" on chr1). From which field does 
> >>>> the table browser retrieve them? It does not seem to be all_mrna.qName, 
> >>>> nor did I find a field in gbCdnaInfo or other soundy tables that are up 
> >>>> to 1-2 joins away from all_mrna. I would need these "_dupX" identifiers 
> >>>> to map back the CDS info I get from hg17.cds to genomic coordinates.
> >>>>
> >>>> Best thanks, micha.
> >>>> _______________________________________________
> >>>> 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

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