hg19 to Broad b37 coordinate conversion

laosaal · 08-28-2012, 03:00 PM

Hi,
We'd like to convert hg19 coordinates to Broad's b37 reference coordinates. For example UCSC's "Known Genes" annotations can only be retrieved in hg19 (or lower) coordinates. b37 sequence differs from hg19 in particular on chrY and the mitochondrial genome.

I've done some searching around here and inquired with various other resources. Liftover seems like a useful tool but I haven't been able to locate a hg19tob37 chain file.

Can anyone recommend a good way forward?

Many thanks in advance,

Lao

TiborNagy · 08-29-2012, 12:33 AM

Well, it is not an easy task, but if you do not need to convert large number of sequences, try Blast/Blat. I have no idea how to handle paralogous regions. (Maybe the order of the genes can help.)

DZhang · 08-29-2012, 07:42 AM

Hi laosaal,

It is not straight forward to do the conversion. Would it be easier for you to redo the analysis using the B37 references? Broad's system is not friendly to hg18/19.

Best regards,
Douglas
www.contigexpress.com

Jim Robinson · 08-31-2012, 05:23 AM

Hi,

Could you elaborate on where you have found differences in chromsome "Y"s sequence? These should be identical between versions you mention.

-- Jim

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08-28-2012, 03:00 PM	#1
laosaal Junior Member Location: Sweden Join Date: Apr 2010 Posts: 2	hg19 to Broad b37 coordinate conversion Hi, We'd like to convert hg19 coordinates to Broad's b37 reference coordinates. For example UCSC's "Known Genes" annotations can only be retrieved in hg19 (or lower) coordinates. b37 sequence differs from hg19 in particular on chrY and the mitochondrial genome. I've done some searching around here and inquired with various other resources. Liftover seems like a useful tool but I haven't been able to locate a hg19tob37 chain file. Can anyone recommend a good way forward? Many thanks in advance, Lao

08-29-2012, 12:33 AM	#2
TiborNagy Senior Member Location: Budapest Join Date: Mar 2010 Posts: 329	Well, it is not an easy task, but if you do not need to convert large number of sequences, try Blast/Blat. I have no idea how to handle paralogous regions. (Maybe the order of the genes can help.)

08-29-2012, 07:42 AM	#3
DZhang Senior Member Location: East Coast, US Join Date: Jun 2010 Posts: 177	Hi laosaal, It is not straight forward to do the conversion. Would it be easier for you to redo the analysis using the B37 references? Broad's system is not friendly to hg18/19. Best regards, Douglas www.contigexpress.com

08-31-2012, 05:23 AM	#4
Jim Robinson Member Location: Boston, MA Join Date: May 2009 Posts: 75	Hi, Could you elaborate on where you have found differences in chromsome "Y"s sequence? These should be identical between versions you mention. -- Jim