Re: [Useq-users] MergeUCSCGeneTable duplicated genes on different chromosomes

[David N. <Dav...@hc...>]

Oh no don't do that!  Gene names are assumed to be unique to the entire
dataset.  I'd suggest prepending the chromosome to your gene name to avoid
collisions.

-cheers, D

On 4/27/12 10:55 AM, "Oler, Andrew (NIH/NIAID) [C]" <and...@ni...>
wrote:

>Hi David,
>
>I noticed something about how MergeUCSCGeneTable treats transcripts with
>the same gene name on different chromosomes.
>
>For example, if I have this UCSC-formatted table:
>cat test.ucsc.real.table
>OR4F16 NM_001005277 chr1 + 367658 368597 367658 368597 1 367658, 368597,
>OR4F16 NM_001005277 chr1 - 621095 622034 621095 622034 1 621095, 622034,
>OR4F16 NM_001005277 chr5 + 180794287 180795226 180794287 180795226 1
>180794287, 180795226,
>
>I run this command to get a merged table:
>
>java -jar ~/USeq/MergeUCSCGeneTable -u test.ucsc.real.table
>
>Arguments: -u test.ucsc.real.table
>
>3 transcripts collapsed to 1 genes.
>
>I get this output:
>
>cat test.real.table_Merged.ucsc
>OR4F16 OR4F16 chr1 + 367658 180795226 367658 180795226 3
>367658,621095,180794287 368597,622034,180795226
>
>I think it should make one merged transcript per chromosome (or else not
>merge them at all since they are far apart and/or don't have any shared
>exons, although not much harm is done by merging them within the same
>chromosome).
>
>Thanks,
>
>Andrew
>
>Andrew Oler, Ph.D.
>High-Throughput Sequencing Bioinformatics Specialist
>Contractor ­ Medical Science & Computing, Inc.
>Computational Biology Section
>Bioinformatics and Computational Biosciences Branch (BCBB)
>OCICB/OSMO/OD/NIAID/NIH
>
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