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
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:
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.
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