Hello Jchl, You are correct --the error message "Deleted in New" means that that region didn't lift. Some things you can do to convince yourself of this are:
--Click into the multiZ alignment page. Scroll down to the "Gap Annotation" subsection of the "Display Conventions and Configuration" section. You will see: "Double line: aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species." --Blat the starting sequence against the other organism I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ----- "jchl tu" <[email protected]> wrote: > Hi everyone: > I use liftover to find conservational regions of human in mouse > genome, and my input data is BED format, and liftover report that > some > of my input data have no retrieves. > below is some of my reports: > #Partially deleted in new > chr2 219233004 219233133 2_219233004_219233133 > #Deleted in new > chr6 99970946 99971025 6_99970946_99971025 > ................... > > and liftover give me its "Explain failure messages", and my question > is do the err reports mean the regions don`t have conservational > counterpart in mouse genome? > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
