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
