cutadapt does something unexpected when i provide a 5' and a 3' adapter sequence

[GoogleCodeExporter]

When I specify 

cutadapt --format=fastq --front='ATGCGTGCTGGTCTCTCGT' 
--adapter='CATTCCGATGAGCGTTCTACAANNNN' input.fastq > both_ends_trimmed.fastq

I expected both ends of my sequence to be cut, but I see mostly the 3' end 
being cut and very little 5' (even though the sequence is obviously present in 
my reads)

When i do cutadapt sequentially, i see the expected output.

cutadapt   --format=fastq --front='ATGCGTGCTGGTCTCTCGT' ' input.fastq > 
step1.fastq
cutadapt   --format=fastq--adapter='CATTCCGATGAGCGTTCTACAANNNN'  step1.fastq > 
both_ends_trimmed.fastq

Am I doing something wrong? Or is the expected behavior?

Brad

Original issue reported on code.google.com by b...@langhorst.com on 1 Oct 2013 at 10:19

[GoogleCodeExporter]

Oh, sorry I've overlooked this for so long. Maybe you've figured it out 
already, but cutadapt trims only one adapter per read in its default settings. 
If you want it to remove two adapters, try to add the parameter --times=2 .

Original comment by marcel.m...@tu-dortmund.de on 9 Feb 2014 at 10:09

[GoogleCodeExporter]

Thanks for the explanation - it makes sense to me know and seems to work fine.

I read the documentation on --times to mean - how many times *each* adapter 
would be trimmed.
At least two of my colleagues here were stymied by the same misinterpretation.

Perhaps a doc update would help others to avoid the same confusion.

Original comment by b...@langhorst.com on 19 Feb 2014 at 2:02