linked adapters in cutadapt
Entering edit mode
5 days ago
Sancar • 0

I need to trim primers from both 5' and 3' ends of PacBio reads. I have a list of such linked adapters in a fasta file. And the primers are not anchored, but both need to be present in a read. The cutadapt documentation (v4.1) mentions "

"If you anchor an adapter, it will also become marked as being required. If a required adapter cannot be found, the read will not be trimmed at all even if the other adapter occurs. If an adapter is not required, it is optional."

It looks like the only way to have both adapters required is to anchor them? Is this possible with the current features of cutadapt? or known workarounds by processing the linked adapter files?

I hope I have not misunderstood what cutadapt is doing with linked adapters.

adapter cutadapt linked • 80 views

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