Hi, I used trinity beta at usegalaxy to assemble my NGS data and received fasta and log file as output. Now for statistical analysis I am trying to use trinity stats.pl through command line. But it’s not working. My question is that for stats analysis both files fasta and log file are required or only fasta file is enough. Second is there any other tool at galaxy for statistical analysis of assembled data.
This tool is not wrapped for Galaxy (yet!).
For alternatives, please see the tutorial at https://galaxyproject.org/learn/ named Intro to Using Galaxy for Bioinformatics. This includes an example Trinity run plus QA/QC for sequence preparation and statistical analysis of the results. Some tools in the tutorial are not available at http://usegalaxy.org but these should all be in the Tool Shed for use in a local/cloud Galaxy.
Help for using the Trinity tool package line-command is at the developer's website here: https://github.com/trinityrnaseq/trinityrnaseq/wiki
Thanks! Jen, Galaxy team
Thanks a lot for providing me information regarding statistical analysis of the trinity results. As you replied that some tools in the are not available at http://usegalaxy.org but these should all be in the Tool Shed for use in a local/cloud Galaxy. My question is that is it possible to use any local/cloud Galaxy from my area as no local galaxy is available here and I am unable to make own galaxy due to shortage of resources. Thx