Question about liftover

[Jessica Grant]

Hello,

I am trying to do a cross-species RNASeq differential expression analysis between two closely related nematodes.  I was hoping to map reads onto the genome of each taxon, and then relate these back to each other as was done in the attached paper.  

Briefly, they use your LiftOver tool, to relate the two genomes, although they are from different species.  The paper is studying primates, and you provide the capability they needed to make their comparison.  We are working with filarial nematodes, with completed genomes.  Would it be possible for me to make the necessary input files myself, to run LiftOver on my taxa?

Please let me know or, if possible, please direct me to the author of the LiftOver tool.

Thanks so much!

Jessica

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Jessica Grant

Research Associate, Williams Lab

205C Ford Hall

Smith College

Northampton, MA 

[Luvina Guruvadoo]

Hello Jessica,

Thanks for your question. We have a number of resources available here:

http://genomewiki.ucsc.edu/index.php/LiftOver_Howto
http://genomewiki.ucsc.edu/index.php/Same_species_lift_over_construction
http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto

Also, feel free to search our Google Groups forum for previously answered questions relating to our liftOver tool:
https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome

I hope this information is useful. 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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[Jessica Grant]

Thank you!  These look like they will help me do what I am trying to do.

Cheers,

Jessica

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