Hello,

I'm new to de novo transcriptome assemblies and have currently completed a strictly de novo assembly using Trinity for a non-model organism. Ultimately, I would like to perform a differential gene expression analysis

I have also generated some gene models but would also like do a genome-guided de novo assembly. I followed the instructions on the Trinity wiki but I am confused by the output.

Each file type has 2 files (a + and - file, ex: all.bam.-.sam.minC1.gff; all.bam.+.sam.minC1.gff)

• What do the + and - represent
• Also, for next steps would I continue with the Trinity pipeline similar to a strictly de novo assembly or a pipeline more geared toward a strictly genome-guided DGE analysis

Thank you in advance