[Useq-users] MergeUCSCGeneTable duplicated genes on different chromosomes

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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)
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