I have tried running synergise2 and for fragment matching I have specified fm.fdr.nonunique = 0.05. Note that I did not specify any argument for fm.minDelta, which defaults to 2. fm.fdr.nonunique and fm.fdr.unique should override fm.minDelta and fm.minCommon respectively
As a result when I run the pipeline with explicit commands I get that 0.05 fdr fm.fdr.nonunique should pick 1 as delta for non-unique fragments, but it does not seem to and even such clear non-unique fragments as:
are still rescue (I specify "rescue" behaviour for nonmatched merged EMRTs)
I have tried running synergise2 and for fragment matching I have specified fm.fdr.nonunique = 0.05. Note that I did not specify any argument for fm.minDelta, which defaults to 2. fm.fdr.nonunique and fm.fdr.unique should override fm.minDelta and fm.minCommon respectively
As a result when I run the pipeline with explicit commands I get that 0.05 fdr fm.fdr.nonunique should pick 1 as delta for non-unique fragments, but it does not seem to and even such clear non-unique fragments as:
are still rescue (I specify "rescue" behaviour for nonmatched merged EMRTs)
The code is in:
Y:\RAW\pvs22_QTOF_DATA_data3\synapter2paper\kuharev2015\bugs_investigation\NP_vs_S2
please have a look.