About decoy peptides

[ypriverol]

@dfermin:

I'm doing some analysis here and I found that when decoys are not exported some of the peptides in the input are not exported, but when the decoys are exported, then they appear.

isDecoy1	isDecoy2	deltaScore	pep1score	pep2score	globalFLR	localFLR
0	0	10.2116	10.2116	0	0.0442	0.0505
0	0	7.5019	7.5019	0	0.0481	0.0723
0	1	5.3761	51.4094	46.0333	0.0659	0.1956

The last peptide will disappear in the first export (default). If I understand correctly is because in the model the second peptide is considered a decoy but what about the first peptide.

[dfermin]

Can you send me the entire output file to look at?