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How does bcl-convert handle UMIs in the 3' end of the insert

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?

umi illumina bcl-convert
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written by ingerslev • ingerslev

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