Hello everyone, I am trying to use Transdecoder output for differential expression analyses:, specifically, Trinity.fasta.cds file with the Trinity build-in script
align_and_estimate_abundance.pl. I would like to perform the analyses at the gene level.
However, the align_and_estimate_abundance.pl with
--trinity_mode only takes headers in default Trinity format (e.g.
TRINITY_DN0_c100_g1_i1) but the headers output from Transdecoder are like
>TRINITY_DN0_c100_g1_i1.p1 TRINITY_DN0_c100_g1~~TRINITY_DN0_c100_g1_i1.p1 ORF type:5prime_partial len:879 (+),score=282.26 TRINITY_DN0_c100_g1_i1:1-2637(+)
I tried to use the headers like
--trinity_mode wouldn't take that as input.
I can get it work by only selecting one gene from
TRINITY_DN0_c100_g1_i1.pX but I lost some ORFs by doing that.
Any suggestions? Thanks in advance!