which file from the Transdecoder.predict to be used for cd-hit input?
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23 months ago
Shahzad ▴ 30

Transdecoder.predict makes following files after completion

  1. transdecoder.assembly.cds
  2. transdecoder.assembly.pep
  3. transdecoder.assembly.bed
  4. transdecoder.assembly.gff3

I want to ask which of this file is to be used with cd-hit for clustering to remove redundant seqs from assembly. if pep file to be used then how to select the relevent seq from the input assembly.

sequencing RNA-Seq Assembly Transdecoder cd-hit • 479 views
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