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alexstaj / cutadapt

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Anchor three-prime adapter #81

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Is it possible to support anchoring of an adapter ligated to the three prime 
end like so?

cat input.fasta
>seq1
SEQSEQSEQTHREEPRIMEADAPTER
>seq2
SEQSEQTHREEPRIMEADAPTERSEQ

cutadapt -a THREEPRIMEADAPTER$ input.fasta

>seq1
SEQSEQSEQ
>seq2
SEQSEQTHREEPRIMEADAPTERSEQ

OS and cutadapt versions:
MacOS_10.9.4; cutadapt1.5

This would be useful in the event paired end reads have been merged, but the 
reads in each file should begin with a known sequence. I realize the dollar 
sign might not work; I include it analogously to the ^ used to indicate the 
beginning of a string. Thanks very much; this program is fantastic!

Original issue reported on code.google.com by jodonnel...@gmail.com on 7 Oct 2014 at 8:27

GoogleCodeExporter commented 9 years ago 
Interesting! It makes sense to support that, but it's not possible right now. I 
may be able to get this implemented for the next version, but I'm not sure how 
long it takes.

Just out of curiosity, which program are you using to merge reads?

Original comment by marcel.m...@tu-dortmund.de on 7 Oct 2014 at 9:00

GoogleCodeExporter commented 9 years ago 
No worries! I can reverse complement sequences and anchor from the other end 
for now. I'm using PEAR to merge reads. Cheers!

Original comment by jodonnel...@gmail.com on 7 Oct 2014 at 9:04

GoogleCodeExporter commented 9 years ago 
Wasn't difficult, so I've just implemented this using the notation you 
suggested (with the dollar sign at the end of the adapter sequence). The docs 
at https://cutadapt.readthedocs.org/ should already reflect this, 
seehttps://cutadapt.readthedocs.org/en/latest/guide.html#anchored-3adapters . 
The change will be part of cutadapt 1.7. Have fun!

Original comment by marcel.m...@tu-dortmund.de on 16 Oct 2014 at 8:26