How does bcl-convert handle reads with an UMI in the 3' end and adapter sequences? The bcl-convert documentation is unclear on the order.
If I set the SampleSheet to contain:
[BCLConvert_Settings] AdapterRead1,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA OverrideCycles,I8;Y48U4
Are the adapters trimmed before UMIs are extracted?
Also for convenience, Is there any way to specify something like
Y*U4 to mean everything except the last 4 bases?