Cutadapt list of adapter
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6.1 years ago
pingEde ▴ 40

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.

 

cutadapt list of adapter trim • 2.3k views
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No, I have not paired reads and I am using 454 Roche Junior

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Try with -b, to see if it finds the sequences 

-b ADAPTER, --anywhere=ADAPTER

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6.1 years ago

If you have paired reads, you can find the adapter sequences using the BBMap package like this:

bbmerge.sh in1=read1.fq in2=read2.fq outa=adapters.fa

But as long as you have standard Illumina adapters, you don't really need to do that...  they will already be in bbmap/resources/adapters.fa

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