dear all:
 i found a problem trimLRPatterns cannot allow this situation
that is the Rpattern has a left shift from subject sequence, see below

subject
 ATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAATATT

Rpattern
AATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG

so i change the code to keep the 5' barcode GCATT, so the pattern can be
recognized


subject
 GCATTATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAATATT

Rpattern
           AATCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG

after remove 3' adaptor, i can remove the 5' barcode

any ideas?

shan gao

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