Cutadapt list of adapter

Question

[pingEde]

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.

Probably the problem is in the parameters that I wrote. In particular I have a list of adapters and 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.

[pingEde]

No, I have not paired reads and I am using 454 Roche Junior

[Sukhi Singh]

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

-b ADAPTER, --anywhere=ADAPTER

Answer 1

[Brian Bushnell]

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