How do I specify alignment targets for the ‘unknown’ bin?
In your config.template.txt file, enter an ELAND_GENOME parameter without any ‘REFERENCE’ specification. This will make it the “default” alignment target for any reads that were not associated with an index/sample (including those that had an index but that couldn’t be matched to the indexes in the sample sheet due to errors), i.e. everything in the ‘unknown’ bin.
