Min abundence question

[EsbergA]

Hi, I am currently using the Emu pipeline, and we have an issue with the --min-abundance command. The --min-abundance can be increased and then Emu generates an output file with the defined threshold. But it does not allow you to give a threshold below 0.0001, which is the default; this will give truncation of samples with a larger number of reads. Is there an option to get it all down to 1 mapped read or a defined 0.000001? / Anders

[kdc10]

You will have to go into the code and change the min abundance (line 302). We don't recommend doing this as we expect many false positives when lowering this threshold.