Transdecoder output for differential expression analyses: header problem
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17 months ago
1215045934 ▴ 40

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_DN0_c100_g1_i1.p1, TRINITY_DN0_c100_g1_i1_p1 but --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!

RNA-Seq Assembly software error genome alignment • 601 views
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Hi, did you find a solution? how did you write the trinity headers after transdecoder? it's happening the same to me. Thanks!

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