About fake reads

From CSBLwiki

3.40) FAKE READS

By "fake reads" I mean reads such as those created from a Genbank reference sequence or a consensus from some other assembly... or others for which there is no chromatogram (and there never was any chromatogram). If you don't use any such reads, you can skip this step.

In the past, any read that ended with a .a2 or .c3 (where 2 and 3 could be any numbers), was considered a fake read. Now you can make Autofinish not assume this using the .consedrc parameter (see CONSED CUSTOMIZATION):

consed.fakeReadsSpecifiedByFilenameExtension: false

Instead, you must have determineReadTypes.perl put "fake" into the "type:" field of a "template" WR item. See determineReadTypes.perl for more information.