I would like to perform a differential gene analysis on a dataset of 120 paird-end files. I obtained a good de novo quality metatranscriptome using rnaSPAdes (83% of the reads aligned exactly 1 time with bowtie2). I would now like to quantify the transcripts by RSEM using Trinity's align_and_estimate_abundance.pl module. When the metatranscriptome is not made with Trinity but another assembler, a --gene-trans-map file must be provided. But I don't know how to obtain this after assembly with rnaSPAdes, I'm having trouble finding this answer on the Internet (I'm a beginner in bioinformatics). Could you explain the steps to follow or the tools to use?
After this I want to group the sample genes counts into a matrix and then use run_DE_analysis.pl and analyze_diff_expr.pl provided by Trinity.