Import multiplexed R1.fastq and R2.fastq with mixed forward and reverse reads + truncate reverse primer

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Hi @thermokarst,

I tested

--p-front CCTACGGGNGGCWGCAG...GGATTAGATACCCBDGTAGTC

and

--p-adapter CCTACGGGNGGCWGCAG...GGATTAGATACCCBDGTAGTC

and both worked!

I also played around with "anchoring" the primers using something like this:

--p-front ^CCTACGGGNGGCWGCAG...GGATTAGATACCCBDGTAGTC$

which resulted in trimming of less sequences.

I am still figuring out the consequences of anchoring, but it is quite well explained in the cutadapt docs here and here and I think I am getting there...

Thanks for forwarding the issues with the documentation and filtering of untrimmed sequences!

Cheers,
Martin

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