Hi Hannah, All Dux'es are still there, they only associated the generic name with the chr18 locus. When you type DUX in the 'gene' cell, you will see the list of all matches (DUX2, DUX4, DUX4L3,DUX4L4 the original chr4 is DUX4L4 and 10 is 4L3 Cheers,
Stephane On 07 Jun 2012, at 21:00, [email protected] wrote: > Send Genome mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.soe.ucsc.edu/mailman/listinfo/genome > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Genome digest..." > > > Today's Topics: > > 1. Re: gff3ToGenePred (Hiram Clawson) > 2. DUX4 (Cheung, Hannah) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 07 Jun 2012 10:20:46 -0700 > From: Hiram Clawson <[email protected]> > Subject: Re: [Genome] gff3ToGenePred > To: Shaun Tyler <[email protected]> > Cc: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Good Morning Shaun: > > Thank you for the example GFF3 files. We will need to fix the gff3ToGenePred > converter program to recognize GFF3 files that do not have mRNA records under > gene records. Our mistaken assumption. > > --Hiram > > Shaun Tyler wrote: >> >> I'm having issues with gff3ToGenePred using GFF files from NCBI. I've seen >> some discussion on this in the archives but no resolution. Initially the >> program threw a few errors due to what turned out to be dashes in some of >> the source description fields. When this was corrected all that was >> generated was an empty file (this was mentioned in the archives). I've run >> the corrected version through the Sequence Ontology Project GFF3 validator >> and it passes with flying colours. Any suggestions would be appreciated. >> >> Shaun > > > ------------------------------ > > Message: 2 > Date: Thu, 7 Jun 2012 13:47:14 -0500 > From: "Cheung, Hannah" <[email protected]> > Subject: [Genome] DUX4 > To: "[email protected]" <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I am trying to search for the genome location of DUX4. I realize that there > is a family of DUX4 genes, but I have also noticed that on hg18, DUX4 is > mapped to chromosomes 10 or 4, while in hg19, it is mapped to chromosome 18. > What is the reason for this? What is the correct location for the gene? > > (Please see enclosed screen captures). > > Thanks, > Hannah Cheung, PhD > Postdoctoral Associate, Plon Lab > President of Baylor College of Medicine Postdoctoral Association > 1102 Bates Ave > Rm.1200.18 > Texas Children's Hospital > Houston, TX 77030 > > ------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > End of Genome Digest, Vol 113, Issue 12 > *************************************** _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
