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Appending barcodes at the end of read names prevent Picard MarkDuplicates from identifying any optical duplicates
Hi Charles,
I just wanted to raise a potential issue with Je. The are two default parameters for Je that cause a potential issue for downstream processing. The default parameters are ADD=TRUE and SAME_HEADERS=TRUE. If you have a paired end read with the following header:
@NB501764:261:HMKKLAFXX:1:11101:3199:1031 1:N:0
This would be converted to
@NB501764:261:HMKKLAFXX:1:11101:3199:1031:BARCODE
Instead of
@NB501764:261:HMKKLAFXX:1:11101:3199:1031 1:N:0:BARCODE
Appending the barcode to cluster coordinates will prevent Picard MarkDuplicates from identifying any optical duplicates.
I hope that makes sense!
Adam