miRDeep in lastest version of Galaxy

Question: miRDeep in lastest version of Galaxy

4.4 years ago by

United Kingdom

Hi,

I was wondering if the new version of Galaxy includes miRDeep in its analysis tools. I've generated BAM files and need to run miRDeep but would like to do it using Galaxy.

Any further info/help appreciated!

Cheers,

Juan Quintana

rna-seq • 1.6k views

ADD COMMENT • link •

modified 3.8 years ago by Bjoern Gruening ♦ 5.1k • written 4.4 years ago by quintanamaster • 20

3.8 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Latest version of mirDeep2 is now included in the Galaxy Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/rnateam/suite_mirdeep_2_0

ADD COMMENT • link written 3.8 years ago by Bjoern Gruening ♦ 5.1k

Dear Bjoern,

Thanks for letting me know. It will come in very handy!

Cheers,

Juan

ADD REPLY • link written 3.8 years ago by quintanamaster • 20

4.4 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi Juan,

we are currently working on the integration of several RNA related tools, including miRDeep2. If you want to help you are welcome!

Cheers,

Bjoern

ADD COMMENT • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k

I'm also interested to analyze my miRNA data in Galaxy with tools like mirDeep2. Just wonder whether text Galaxy could be incorporated with mirDeep2 or give a provision for installing from Toolshed.

ADD REPLY • link written 4.2 years ago by sabuknair • 0

The plan is to add a wrapper for mirDeep2 and add it to the toolshed. But I'm a little bit busy these days. If you want to learn how to wrap tools, I can help you if you like.

Cheers,

Bjoern

ADD REPLY • link written 4.2 years ago by Bjoern Gruening ♦ 5.1k

4.4 years ago by

quintanamaster • 20

United Kingdom

quintanamaster • 20 wrote:

Hi Bjoern,

Thanks for your answer! How can I be helpful?

Cheers,

Juan

ADD COMMENT • link written 4.4 years ago by quintanamaster • 20

Are you a developer? Than you can help to write the wrapper, if you are an user you can help to test them at some point :)

ADD REPLY • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k

I'm a user with some degree of expertise on Galaxy, so I'd be glad to test it. Got lots of datasets awaiting for such analysis.

ADD REPLY • link written 4.4 years ago by quintanamaster • 20

I will try to prioritize it a little bit higher, but can't promise much.

Keep an eye on: https://github.com/bgruening/galaxytools especially the RNA folder.

Cheers,

Bjoern

ADD REPLY • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k

Will do,

Thanks for replying and prioritising, I think it'll make a huge improvement on Galaxy if we get to make miRDeep available as well.

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