Hello Peng, Please note in the earlier message that the data was moved: > data comes from http://polya.umdnj.edu (redirects to: > http://polya.umdnj.edu/polyadb/). They provide both a Poly(A) > database and Poly(A) site prediction and analysis tools.
If I go to the link: http://polya.umdnj.edu/polyadb/ The databases contain information about mouse. If you having trouble locating the download file, the suggestion is use the contact information at the bottom of the page. They would be able to offer you specific help for their web site/data. Thanks, Jen ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Peng Yu" <[email protected]> wrote: > From: "Peng Yu" <[email protected]> > To: "Jennifer Jackson" <[email protected]>, [email protected] > Sent: Friday, January 22, 2010 9:21:37 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Mouse PolyA site > > On Fri, Jan 22, 2010 at 2:18 PM, Jennifer Jackson <[email protected]> > wrote: > > Hi Peng, > > > > We are sorry for the inconvenience, but this track has not been > marked for development considering our other priorities. > > > > Some details so that you can obtain/create the data yourself: > > > > By reviewing the hg18 make doc (in the kent source tree at > kent/src/hg/makeDb/doc/hg18.txt), you can find all the details of how > the track was created for human and use this as a model for mouse. The > data comes from http://polya.umdnj.edu (redirects to: > http://polya.umdnj.edu/polyadb/). They provide both a Poly(A) > database and Poly(A) site prediction and analysis tools. > > Hi Jen, > > The data file is not accessible anymore. > > http://polya.umdnj.edu/download/polyAsite.gz > > I also don't find the data file for mouse. Do you know where to > download them? > > Regards, > Peng > > > ############################################################################ > > # POLYA_DB TRACK (DONE 08-28-2006 Andy) > > > > mkdir /cluster/data/hg18/bed/polyaDB > > cd /cluster/data/hg18/bed/polyaDB > > wget http://polya.umdnj.edu/download/polyAsite.gz > > gunzip polyAsite.gz > > find /cluster/data/hg16/ -name 'ordered.lft' | xargs cat > hg16.lft > > sed 's/\(\s\).*\//\1/; s/chr/hg16.chr/' hg16.lft > tmp > > mv tmp hg16.lft > > cut -f2 hg16.lft > hg16.lft.names > > grep -F -f hg16.lft.names polyAsite > hg16.polyAsite > > awk '{printf("%s\t%d\t%d\t%s\n", $3, ($5-1), $5, $1);}' > hg16.polyAsite > > > hg16.polyAsite.bed > > liftUp lifted.bed hg16.lft warn hg16.polyAsite.bed > > sed 's/hg16\.//' lifted.bed > final.bed > > liftOver final.bed /gbdb/hg16/liftOver/hg16ToHg18.over.chain.gz > hg18.bed unmapped > > hgLoadBed hg18 polyaDB hg18.bed > > # trackDb entry/html in human/hg18 > > > > > > ------------------------------------------------ > > Jennifer Jackson > > UCSC Genome Bioinformatics Group > > > > ----- "Peng Yu" <[email protected]> wrote: > > > >> From: "Peng Yu" <[email protected]> > >> To: "Jennifer Jackson" <[email protected]> > >> Sent: Thursday, January 21, 2010 8:20:50 AM GMT -08:00 US/Canada > Pacific > >> Subject: Re: [Genome] Mouse PolyA site > >> > >> On Wed, Jan 20, 2010 at 8:46 PM, Jennifer Jackson > <[email protected]> > >> wrote: > >> > Hi Peng, > >> > > >> > We will not be creating this track for mouse. Perhaps by > examining > >> the methods/publications in the hg18 database, you can create the > data > >> yourself, and load as a custom track. > >> > >> Hi Jen, > >> > >> Would you please let me know why your group make this decision? > >> > >> Regards, > >> Peng > >> > >> > Very sorry for the inconvenience, > >> > Jennifer > >> > > >> > > >> > ------------------------------------------------ > >> > Jennifer Jackson > >> > UCSC Genome Bioinformatics Group > >> > > >> > ----- "Peng Yu" <[email protected]> wrote: > >> > > >> >> From: "Peng Yu" <[email protected]> > >> >> To: [email protected] > >> >> Sent: Wednesday, January 20, 2010 4:05:38 PM GMT -08:00 > US/Canada > >> Pacific > >> >> Subject: [Genome] Mouse PolyA site > >> >> > >> >> There is the Poly(A) Sites track for human. But it is not > >> available > >> >> for mouse. Could somebody make one for mouse? > >> >> _______________________________________________ > >> >> Genome maillist - [email protected] > >> >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > >> > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
