FDR, Decoy Hits, and Forward/Decoy FASTAs in Scaffold

If the search engine tool (eg, MQ, Mascot, PD, etc) has an on-the-fly decoy function (wherein it reverses or randomizes the FASTA while it searches, and performs a decoy search at the same time), and this function was used in the search, then you do not use a forward/decoy concatenated FASTA in Scaffold. In this case, simply use the same forward FASTA you used in the search.

If the on-the-fly decoy function is not available or wasn't used, and you want to get decoys, then you must use a forward/decoy concatenated FASTA in both the search engine and Scaffold to get decoys.

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