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Question: where is the de novo assembler?
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gravatar for weiqi.wang1983
4.1 years ago by
weiqi.wang1983 • 0
United States
weiqi.wang1983 • 0 wrote:

hi, first of all thanks for your hard work! I'm trying to do a de novo assembly of a mouse transcriptome but did not find a de novo assembler. I did see one called "trinity" though, from your tutorial video (yet the GUI in the video is out-dated so the current GUI does not have it). So my question is where is the de novo assembler(s) please?

Also another question: what's the differences of mm10 and mm9 etc.? For my specific project I wanna analyze mouse whole transcriptome, should I use mm10 or mm9 please?

Looking forward to your reply, thanks a lot!

 

weiqi
assembly alignment rna-seq de novo assembler • 1.0k views
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modified 4.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.1 years ago by weiqi.wang1983 • 0
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gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For assembly tools, now please see the Tool Shed. This work will need to be done on a local or cloud Galaxy.
http://usegalaxy.org/toolshed
http://wiki.galaxyproject.org/BigPicture/Choices

The two mouse genomes you mention are two releases of the same assembly. The newer one is mm10. Full details about each are available at the data source: UCSC http://genome.ucsc.edu

Take care, Jen, Galaxy team
ADD COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k
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