UCSC Display option

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UCSC Display option

nephantes
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: [hidden email]




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Re: UCSC Display option

Hans-Rudolf Hotz
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: [hidden email]
>
>
>
>
> ___________________________________________________________
> 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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Fwd: UCSC Display option

nephantes
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: [hidden email]



Begin forwarded message:

From: Hans-Rudolf Hotz <[hidden email]>
Subject: Re: [galaxy-dev] UCSC Display option
Date: February 27, 2014 at 3:57:36 AM EST
To: Alper Kucukural <[hidden email]>, Galaxy Dev <[hidden email]>

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: [hidden email]




___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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___________________________________________________________
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/