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Question: Can Galaxy be used for straned RNA seq analysis
1
gravatar for youyouzh
4.4 years ago by
youyouzh • 10
United States
youyouzh • 10 wrote:

My question is as the title. I am wondering whether galaxy can be used for the stranded RNA-seq analysis. Thanks a lot.

Youyou
rna-seq • 1.2k views
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modified 4.4 years ago by Suzanne Gomes • 120 • written 4.4 years ago by youyouzh • 10
2
gravatar for Suzanne Gomes
4.4 years ago by
Suzanne Gomes • 120
Canada
Suzanne Gomes • 120 wrote:

If you mean 'Can Galaxy be used to analyze RNA-seq data with strand-of-origin information', then yes, it can. If you are using TopHat to align your reads to a reference genome, then under 'library type' you can select either 'FR First strand' or 'FR Second strand', depending on the protocol that was used to create your library. 
ADD COMMENT • link written 4.4 years ago by Suzanne Gomes • 120

Hi Galaxy Thanks for your reply and helpful information. Can galaxy be used for the analysis of circular RNA. Thanks a lot. Youyou

ADD REPLY • link written 4.4 years ago by youyouzh • 10
1

Just as a small remark. Galaxy can be used for literally everything. Your tools need to support it. If you have tools for that, you can search if there are wrappers for it, otherwise you can integrate them by your own.

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

Hi Youyou, Would you please start this as a new question? That'll help folks to both find the question to answer it, and others to read the reply once posted. Thanks! Jen, Galaxy team

ADD REPLY • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k

Also, if a reply has answered your question, it helps greatly to mark it as "accepted". As the original question poster, you are the only one that can do this. Anyone else reading - this applies to all Q&A - and over time this will help to focus the forum on the answers that address/resolve the questions asked. "Upvotes" by the rest of the community can only help promote good answer so much. Thanks from the Galaxy team! Jen

ADD REPLY • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k
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