Add a new reference genome

Question: Add a new reference genome

4.1 years ago by

small • 0

small • 0 wrote:

Dear sir,

Sorry to bother you. I am not sure it is right to contact with you, but i need some helps. Now, i plan to map our RNA-seq data of wheat to the wheat reference genome using the Tophat tool intergated into Galaxy. At present, the wheat genome is not included in the Galaxy database. I saw a sentence like this in Galaxy interface "If your genome of interest is not listed, contact the Galaxy team". So , i am writing to ask whether it is possible to add the wheat genome (http://ensembl.gramene.org/Triticum_aestivum/Info/Index)(Triticum_aestivum.IWGSP1.23) to Galaxy database. Thanks!

Best Regards,

Sincerely yours

Xiaojun Nie

rna-seq tophat • 1.5k views

ADD COMMENT • link •

modified 23 months ago by jiangdan • 0 • written 4.1 years ago by small • 0

4.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I have added this genome to the request list at Trello:
https://trello.com/c/mJWnAuuQ

But you do not need to wait for this. Use the reference genome as a Custom Reference genome with tools now. Instructions are here, including how to add this as a "Custom Build" so that the database attribute can be assigned (optional for some tools, required for others).
http://wiki.galaxyproject.org/Support#Custom_reference_genome

Best, Jen, Galaxy team

ADD COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k

OK，thanks very much for your kind help.Thanks!
NXJ
-----------------------
Nie Xiaojun
College of Agronomy
NWSUAF, Yangling-712100
P R CHINA
Cell:13468846103
</quark_editor_sign><quark_editor_card></quark_editor_card>-------- 原始邮件 --------
发件人: Jennifer Hillman Jackson on Galaxy Biostar<notifications@biostars.org>
发送时间: 2014-11-07 23:04
收件人: small@nwsuaf.edu.cn
主　题: Re:[galaxy-biostar] A: Add a new reference genome

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User Jennifer Hillman Jackson wrote A: Add a new reference genome:

Hello,

I have added this genome to the request list at Trello:
https://trello.com/c/mJWnAuuQ

But you do not need to wait for this. Use the reference genome as a Custom Reference genome with tools now. Instructions are here, including how to add this as a 'Custom Build' so that the database attribute can be assigned (optional for some tools, required for others).
http://wiki.galaxyproject.org/Support#Custom_reference_genome

Best, Jen, Galaxy team

You may reply via email or visit A: Add a new reference genome

ADD REPLY • link written 4.1 years ago by small • 0

23 months ago by

jiangdan • 0

jiangdan • 0 wrote:

Dear sir,

Sorry to bother you. I am not sure it is right to contact with you, but i need some helps. Now, I plan to map our chip_seq data of fly to the fly reference genome using the Bowtie tool intergated into Galaxy. At present, the fly genome is not included in the Galaxy database. I saw a sentence like this in Galaxy interface "If your genome of interest is not listed, contact the Galaxy team". So , i am writing to ask whether it is possible to add the fly genome (http://genome.ucsc.edu/cgi-bin/hgTables) to Galaxy database. Thank you!

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