Yes, that worked, Thanks, Alper Kucukural, PhD Bioinformatics Core, University of Massachusetts Medical School 368 Plantation St.Room AS4.2067 Worcester, MA 01605-2324 Phone: 774-312-4493 E-mail: [email protected]
Begin forwarded message: > From: Hans-Rudolf Hotz <[email protected]> > Subject: Re: [galaxy-dev] UCSC Display option > Date: February 27, 2014 at 3:57:36 AM EST > To: Alper Kucukural <[email protected]>, Galaxy Dev <[email protected]> > > Hi Alper > > > Have a look at ~/galaxy_dist/tool-data/shared/ucsc/ucsc_build_sites.txt > > check the line starting with > > "main http://genome.ucsc.edu/cgi-bin/hgTracks?"; > > and add mm10 > > > do a restart and you should get the link to 'UCSC main' for data mapped to > mm10 > > > if that fixes the problem for UCSC, you can do the same for ensembl by fixing: > > galaxy_dist/tool-data/shared/ensembl/ensembl_sites.txt > > > > Regards, Hans-Rudolf > > > > > > > On 02/26/2014 08:01 PM, Alper Kucukural wrote: >> Hi, >> >> When I map the reads with bowtie2 to hg19. >> I got the output like below and there are four display options. When I map >> the reads to mm10. I got only display in “IGB Local Web option". So, how can >> I fix this for mm10 or others and show all options? >> >> 101: Bowtie2 on data 4: aligned reads >> 91.6 KB >> format: bam, database: hg18 >> [bam_header_read] EOF marker is absent. The input is probably truncated. >> [samopen] SAM header is present: 45 sequences. 2500 reads; of these: 2500 >> (100.00%) were unpaired; of these: 1829 (73.16%) aligned 0 times 279 >> (11.16%) aligned exactly 1 >> display at UCSC main test >> display at Ensembl May 2009 >> display with IGV web current local >> display in IGB Local Web >> >> Best, >> >> Alper Kucukural, PhD >> Bioinformatics Core, >> University of Massachusetts Medical School >> 368 Plantation St.Room AS4.2067 >> Worcester, MA 01605-2324 >> Phone: 774-312-4493 >> E-mail: [email protected] >> >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >>
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