Question: where is the de novo assembler?
0
gravatar for weiqi.wang1983
3.3 years ago by
United States
weiqi.wang19830 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

ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson23k • written 3.3 years ago by weiqi.wang19830
0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 98 users visited in the last hour