Can you provide some more information on your pipeline? Did you map your reads to a genome?
Please have a look at the tutorials here for recommended pipelines to use for RNA-seq analysis: http://galaxyproject.github.io/training-material/topics/transcriptomics/
Thanks for using Galaxy!
I ran my RNA sequencing data through Trinity for de novo transcriptome assembly. I am currently running Tophat for my samples because the files from Trinity could not be read by Cufflinks. My organism is a frog called Hymenochirus boettgeri, related to Xenopus, and I want to do transcriptome annotation to find a gene sequence of a pheromone from the breeding gland of the frog. I took a look at the pipelines provided in the link and they did not use Trinity as part of it. Are there any pipelines you recommend that use Trinity? Also, my samples were sent to FGL of QB3 Berkelely. Is the quality control step still necessary? Thank you so much.
Trinity will output transcript sequences in fasta format. You can use these sequences as a reference for tools to quantify transcript expression levels. Perhaps you could try using Salmon to quantify expression levels.
You should always do QC on your samples.
Good luck hunting for your pheromone!
Cheers, Mo Heydarian