Cutadapt, list of adapter

[pingu]

Hello,

I am using Cutadapt, but I have a problem: It doesn't find adapter, but with a banal research with function "find" in the file I find adapters, so I am sure that they are in my file.

Probabily the problem is in the parameters that I wrote. In particular I have a list of adapterand I have to trim at 5'. I wrote this:

cutadapt -g adapter.fasta -o output.fastq myfile.fastq

What is the problem? Please could you help me?

Thank you in advance.

[GenoMax]

Have you tried the anchored 5'-adapter removal option (-g ^adapter)? That should recognize partial pieces (as noted here http://cutadapt.readthedocs.org/en/latest/guide.html). This will only work if your adapter starts right at base 1.

[GenoMax]

You may also want to take a look at BBDuk.sh which is part of BBMap suite.

[pingu]

Have you tried the anchored 5'-adapter removal option (-g ^adapter)? That should recognize partial pieces (as noted here http://cutadapt.readthedocs.org/en/latest/guide.html). This will only work if your adapter starts right at base 1.

Thank you for your response, yes I have tried also the anchored 5'-adapter removal option. If I use a single adapter Cutadapt trims, so I think that the problem is when I use a list of adapter...

[GenoMax]

Thank you for your response, yes I have tried also the anchored 5'-adapter removal option. If I use a single adapter Cutadapt trims, so I think that the problem is when I use a list of adapter...

Are you providing the adapters with an individual -g for each adapter? You could also put them in a file as described in the help doc. Click on the multiple adapters link in left navigation pane.

$ cutadapt -g file:adapters.fasta -o output.fastq input.fastq

[pingu]

Thank you for your response. I have tried use that command. I think that probably the problem is in the structure of my file with adapter. Please could you write me an example of the structure?
Thank you very much in advance