[Genome] Converting coordinates on a mRNA to coordinates on the genome

[Rachel Harte]

Hello Archie,

We have a tool called pslMap which is in the directory,
src/hg/pslMap/, in the Genome Browser source tree that will help you
do this calculation. If you type pslMap at the command line, you will get
help for using the program.

The input files should be in PSL format - see
http://genome.ucsc.edu/FAQ/FAQformat#format2

You should create a PSL file of coordinates for your mRNAs as the inPsl
and then the mapPsl should be a PSL file of mRNA alignments to a
genome downloaded from our downloads server:

http://hgdownload.cse.ucsc.edu

Click on the organism of interest, find the correct assembly, and then
click on the "Annotation database" link.

all_mrna.txt.gz is the PSL file of mRNA alignments and refSeqAli.txt.gz is
the PSL file for RefSeq mRNA alignments.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

 Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Tue, 3 Jul 2007, Russell, Archie wrote:

>
> Hi,
>
> I have some coordinates relative to mRNAs (transcript features) that I'd
> like to turn into coordinates on the genome.   I can blat the mRNA to
> the genome, but doing the math for the translation is a little tricky,
> in particular on the reverse strand.   Do you have any code or
> recommendations for how to do this?
>
> Thanks,
> Archie
>
>
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