I am running both using command line. My problem is that if I take the same coordinates in genepred format but otherwise the same command using the minMatch=0.1 they won't liftover, but if I take those coordinates and put them in a bed format all the coordinates liftover. I am confused why there is a difference when the coordinates are the same only the format has changed.
On 3/6/12 6:33 PM, "Vanessa Kirkup Swing" <[email protected]> wrote: Hi Allissa, This is likely due to the "Minimum ratio of bases that must remap" setting for the web version or if you are using the command line version it is the "minMatch" setting. Please see this previously answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2011-April/025613.html If you have further questions, please email the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Dillman, Allissa (NIH/NIA/IRP) [F] <[email protected]> Date: Tue, Mar 6, 2012 at 9:15 AM Subject: [Genome] Liftover help To: "[email protected]" <[email protected]> Hello I am having some discrepancies using the liftover tool When I run the liftover tool using these coordinates: chr17:26900132-26900639 chr17:26900752-26900952 chr17:26901084-26901259 chr17:26901511-26901595 chr17:26901713-26901874 chr17:26901969-26902024 chr17:26902140-26902352 chr17:26902438-26902562 chr17:26903818-26903952 Going from human to macaque all sites liftover. When I run the liftover command using a file which contains these coordinates as one gene in genephred format or bed format I get an error saying # Partially deleted in new. Why is there a difference? _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome ------ End of Forwarded Message _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
