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Closed
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Opened Jul 24, 2017 by Charles Girardot@girardotOwner

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

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Reference: grp-gbcs/Je#2