Clipping of KAPA adapters · Biostar

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Clipping of KAPA adapters

Dear colleagues,

could you please help me with an issue. Can Trimmomatic delete KAPA hyper plus adapters from sequencing reads? I know adapter sequence and hope it could be done like in Cutadapt (i.e. set an arbitrary sequence, not from those listed in Trimmomatic adapter folder). But when I try to input my adapter file, Trimmomatic quits with an error. What should I do (except using cutadapt)?

assembly

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written 6.1 years ago by mewgia •

But when I try to input my adapter file, Trimmomatic quits with an error.

What kind of an error?

You can also use bbduk.sh from BBtools. Specify a file with adapters to scan by using ref=adapter.fa. Guide available here.

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written 6.1 years ago by GenoMax

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