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.
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.
1 answer
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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No, I have not paired reads and I am using 454 Roche Junior
Try with
-b, to see if it finds the sequences