Hi everybody,

I have performed de novo assemblies of two non-model species using Trinity and I've used the Trinotate pipeline to get the annotation report of both of them. Now, I want to perform a differential expression analysis between the two species (same tissue), but I have somo problems:

1. I have two Trinity.fasta files with my sequences as named by Trinity (e.g: >c0_g1_i1 len=1748 path=[45:0-1747]) and two Trinotate reports in .xls format. Does anybody know how to get a .fasta file with the sequence names obtained by Trinotate? If I don't change the names, the sequence corresponding to any name (e.g: >c0_g1_i1 len=1748 path=[45:0-1747]), will not be the same in the two fasta files, and thus I will not be able to perform a DE analysis (as they don't use the sequence itself but the sequence's name).
2. Does anybody knows a tool for between species DE analysis? I've been looking at the Trinity pipeline and seem good, but to use it I need to solve the first problem. I don't know if more specific tools exist.

Any help will be great.

Thanks,
Guillermo