Yes, that worked,
Alper Kucukural, PhD
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
Begin forwarded message:
> From: Hans-Rudolf Hotz <h...@fmi.ch>
> Subject: Re: [galaxy-dev] UCSC Display option
> Date: February 27, 2014 at 3:57:36 AM EST
> To: Alper Kucukural <al...@kucukural.com>, Galaxy Dev <galaxy-...@bx.psu.edu>
> 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
> if that fixes the problem for UCSC, you can do the same for ensembl by fixing:
> Regards, Hans-Rudolf
> On 02/26/2014 08:01 PM, Alper Kucukural wrote:
>> 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
>> 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: al...@kucukural.com
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