Hi, I'm forwarding an email from a Galaxy user, which points out a possible discrepancy in the outputs obtained by using liftOver binary downloaded from UCSC versus liftOver utility available on UCSC website. There is also a sample input file attached, which produces different outputs in the 2 cases. Can you please advise us on why this could be happening?
Thanks, Guru. Galaxy Team. Begin forwarded message: > From: "GALIH Kunarso" <[email protected]> > Date: March 25, 2009 5:11:12 AM EDT > To: <[email protected]> > Subject: [galaxy-bugs] liftOver discrepancy > > Hi Galaxy, > > Firstly, thanks for your nice website, it’s very useful and I use > it a lot! > > I would like to highlight to you here a difference between the > liftOver results from your main site to the one I got from the UCSC > site. > > For example, I attach here 100bp-long regions surrounding the Oct4 > binding site identified by ChIP-Seq in mouse Embryonic Stem cell > (Chen X, Xu H, et al. Integration of external signaling pathways > with the core transcriptional network in embryonic stem cells. > Cell. 2008 Jun 13;133(6):1106-17). > > When I liftOver-ed this using the main Galaxy site from mm8 to hg18 > I got 1651 successful conversions and 2110 Unmapped coordinates. > When I tried this on UCSC site I got back 2496 successful > conversions and 1265 failures. I just used the default parameter of > the UCSC site for this (Minimum ratio of bases that must remap: > 0.1, Minimum chain size in target: 0, Minimum hit size in query: 0, > Allow multiple output regions: Unticked, Min ratio of alignment > blocks/exons that must map: 1, If thickStart/thickEnd is not > mapped, use the closest mapped base: Unticked). > > Based on my simple checking, some of Galaxy’s “#Partially > deleted in new” are considered as success by UCSC. > > Can you help me regarding this? Is your liftOver parameter > different from the default UCSC one? > > Thank you for your attention. > > > Regards, > > Galih Kunarso > Computational and Mathematical Biology > Genome Institute of Singapore > 60 Biopolis Street, Genome #02-01, Singapore 138672 > DID: 6478-8661 Fax: 6478-9058 > > -------------------------------------------------------- > This e-mail is confidential and may be privileged. If you > are not the intended recipient, please delete it and notify > us immediately. Please do not copy or use it for any purpose, > or disclose its contents to any other person. Thank you. > -------------------------------------------------------- >  > _______________________________________________ > galaxy-bugs mailing list > [email protected] > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-bugs Regards, Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
