hg19 to Broad b37 coordinate conversion

[Lao Saal]

To whom it may concern:

We are interested in analyzing RNA-seq data using the Broad b37
reference genome in conjunction with the "Known Genes" UCSC annotations.
The Known Genes track appears to be quite a bit more comprehensive
than e.g. RefSeq genes.

The problem we have is that these annotations are in hg19, and I'm not
sure the best way to convert them to the b37 coordinates. For example,
I can't locate a chain file for hg19tob37.

I wonder what the best way to convert hg19 to b37? Or is there
available already a GTF file (or similar) with the Known Genes using the
b37 reference coordinates?

Or can someone point me towards someone who might be able to assist?

Many thanks in advance,

Lao

---
Lao Saal, M.D. Ph.D.
Head, Translational Oncogenomics Unit
Asst. Professor, Department of Oncology
CREATE Health Centre, BMC C1322b
Lund University
SE-22184, Lund, Sweden
tel: +46-46-2220365
fax: +46-46-147327
email: lao....@med.lu.se

[Steve Heitner]

Hello, Lao.

We do not support the b37 assembly. Typically, we only support the NCBI
default assembly for any given organism. In this case for human, we only
support the GRCh37 assembly. You may want to consider creating your own
liftOver file, though. The previously-answered mailing list question at
https://lists.soe.ucsc.edu/pipermail/genome/2010-January/020985.html has
several links to useful information to assist you in this.

Please contact us again at gen...@soe.ucsc.edu if you have any further
questions.

---
Steve Heitner
UCSC Genome Bioinformatics Group

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