Question: Can Galaxy be used for straned RNA seq analysis
1
gravatar for youyouzh
4.4 years ago by
youyouzh10
United States
youyouzh10 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
ADD COMMENTlink modified 4.4 years ago by Suzanne Gomes120 • written 4.4 years ago by youyouzh10
2
gravatar for Suzanne Gomes
4.4 years ago by
Suzanne Gomes120
Canada
Suzanne Gomes120 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 COMMENTlink written 4.4 years ago by Suzanne Gomes120

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

ADD REPLYlink written 4.4 years ago by youyouzh10
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 REPLYlink written 4.4 years ago by Bjoern Gruening5.1k

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 REPLYlink written 4.4 years ago by Jennifer Hillman Jackson25k

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 REPLYlink written 4.4 years ago by Jennifer Hillman Jackson25k
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