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: alper@kucukural.com
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/