Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: trinity statistical analysis
0
gravatar for humairawahid
19 months ago by
humairawahid • 0
humairawahid • 0 wrote:

Hi I am new trinity user at usegalaxy. I used trinity to assemble my NGS data and received fasta fie as output. Now I need statistical analysis for number of genes,transcripts, N50 etc. kindly guide me how to perform this analysis using galaxy. thx
assembly • 591 views
ADD COMMENT • link •
modified 19 months ago by rachelrodgers12 • 20 • written 19 months ago by humairawahid • 0
2
gravatar for rachelrodgers12
19 months ago by
rachelrodgers12 • 20
rachelrodgers12 • 20 wrote:

Hi, there is a Trinity script called TrinityStats.pl that may tell you what you want, but I don't know how it's accessed in Galaxy. Maybe this post will be useful for you:

https://www.biostars.org/p/200187/

In any case you can easily download this Perl script and simply run it on your Trinity results file that you've produced in Galaxy.
ADD COMMENT • link written 19 months ago by rachelrodgers12 • 20
0
gravatar for Jennifer Hillman Jackson
19 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Galaxy tutorials and tours are listed here: https://galaxyproject.org/learn/

You might want to start with the one under "Tutorials from around the Web" named "Intro to Using Galaxy for Bioinformatics > Includes a transcriptome assembly example". Some of the tools in this particular example are only available for use in a local Galaxy (BLAST is not at http://usegalaxy.org), but this should give you the general idea of how to investigate your assembly results.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour