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jgaetel / cutadapt

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I'd like to be able to trim partial adapter sequence from the 5' end as happens with the 3' end. Is that possible? #58

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I'm using the Truseq kit for RNAseq and find varying amounts of the universal 
adapter on the 5' end of my reads as well as the indexed adapter on the 3' end. 
In a test file I placed several sequenced including both universal sequence on 
the 5' and indexed on the 3'. Cutadapt works great for the 3' end, and trimmed 
the correct amount of sequence from the three sequences containing the indexed 
adapter. However, for the universal adapter on the 5' end, only the read with 
the longest sequence, similar to the entire adapter was trimmed, although two 
other reads contained part of the universal adapter.

Thanks very much - more details below.

Testfile Description

16 sequences

1-10 no adapter sequence

sequence 11 has univ seq ATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT 
at 5' end, trimmed
sequence 12 has univ seq CTCTTCCGATCT at 5' end, not trimmed
sequence 13 has univ seq ACACGACGCTCTTCCGATCT at 5' end, not trimmed
sequence 14 has indexseq GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCT at 3' end, 
trimmed
sequence 15 has indexseq GATCGGAAGAGCACACGTCTGAACTCCAG at 3' end, trimmed
sequence 16 has indexseq GATCGGAAGAG at 3' end, trimmed

Original issue reported on code.google.com by blarison...@gtempaccount.com on 27 Dec 2012 at 4:15

GoogleCodeExporter commented 9 years ago 
Partial adapter matches in the 5' end are possible. Could you please tell me 
exactly which cutadapt command-line you used? Also, do you have a small FASTQ 
file that shows the problem?

Original comment by marcel.m...@tu-dortmund.de on 27 Dec 2012 at 12:25

GoogleCodeExporter commented 9 years ago 
I originally used -g with the adapter anchored (^) to the 5' end, but then 
discovered your newer -b option which seems to correctly removed partial 
adapter sequences from the 5' end. So I think I'm set as far as that is 
concerned. Thanks!

Original comment by blarison...@gtempaccount.com on 28 Dec 2012 at 6:53

GoogleCodeExporter commented 9 years ago 
Great! Just one comment: The '-b' option is for adapters that may be in the 3' 
or in the 5' end. It may give better results if you use the '-g' option without 
anchoring.

Original comment by marcel.m...@tu-dortmund.de on 28 Dec 2012 at 9:48