Question: trinity statistical analysis
gravatar for humairawahid
19 months ago by
humairawahid0 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 COMMENTlink modified 19 months ago by rachelrodgers1220 • written 19 months ago by humairawahid0
gravatar for rachelrodgers12
19 months ago by
rachelrodgers1220 wrote:

Hi, there is a Trinity script called 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:

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 COMMENTlink written 19 months ago by rachelrodgers1220
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Galaxy tutorials and tours are listed here:

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, but this should give you the general idea of how to investigate your assembly results.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 19 months ago by Jennifer Hillman Jackson25k
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