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  • Cutadapt, list of adapter

    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.

  • #2
    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.

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    • #3
      You may also want to take a look at BBDuk.sh which is part of BBMap suite.

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      • #4
        Originally posted by GenoMax View Post
        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...

        Comment


        • #5
          Originally posted by pingu View Post
          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.

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

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          • #6
            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

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