which file from the Transdecoder.predict to be used for cd-hit input?

Question

[Shahzad]

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.