hgLiftover

[Brian Smith]

Hi,

I was trying to convert a bed file from Mouse (mm9) to Human (hg19). The bed file has about 80,000 rows and the hgLiftOver tool seems to hang. Even after a few hours, there are no results (screenshot of what I get is here: http://screencast.com/t/lXOB8M9f).

If I take a few thousand rows from the bed file and c&p it directly into the box and click 'submit' it works just fine. Again, if I c&p all the 80,000 rows, then it hangs again.

My questions:

1. Is there a max limit on the number of rows in the bed file (or timeout limit)?

2. If I have to download the executable, which chain file do I need to convert from mouse (mm9) to human (hg19)?

many thanks!

[Luvina Guruvadoo]

Hello Brian,

Thank you for your question. There is no limit that we know of, however for large queries such as yours, we recommend using the liftOver executable. The chain file you will need is mm9ToHg19.over.chain.gz, which you can download from this directory: http://hgdownload.soe.ucsc.edu/goldenPath/mm9/liftOver/

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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[Brian Smith]

Thanks! Is there a manual or README file that will help me with the installation and usage?

regards,

[Steve Heitner]

Hello, Brian.

The executable file is available at http://hgdownload.cse.ucsc.edu/admin/exe/.  It is a standalone executable and requires no installation.  There is no README, but if you run the command with no arguments, the usage statement is displayed.  Note that in the usage, “oldFile” and “map.chain” are your two input files and “newFile” and “unMapped” are your two output files.  The “unMapped” file will contain any coordinates that could not be converted from mouse to human.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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