Cut-adapt trim paired - different results when primers separate vs linked


I am getting different results when I list my primers separately vs listing them as linked. Linked, both are removed correctly, but listed separately, the forward primers are not being removed.

Specifically, this script removes both forward and reverse primers:

qiime cutadapt trim-paired
–i-demultiplexed-sequences Mini_test/demultiplexed_sequences.qza
–o-trimmed-sequences Mini_test/demultiplexed_trimmed_sequences_8.qza \

But this script is only removing the reverse primers:

qiime cutadapt trim-paired
–i-demultiplexed-sequences Mini_test/demultiplexed_sequences.qza
–o-trimmed-sequences Mini_test/demultiplexed_trimmed_sequences_7.qza \

Ideally, I would like to run them separately, because I would like to discard any sequences missing the forward primer, since these are probably no good, but retain sequences that are only missing the reverse primer, since these might be the result of biologically meaningful length variation in the amplicon. (I tried specifying the reverse of the linked primers as optional - “;optional”, as per the cut-adapt website, but that made all kinds of errors)

Any insight into where I’m going wrong would be much appreciated!

1 Like

Solved it!

Apparently it can’t handle too many separate things at once - running forwards and reverses as two separate commands gave the expected trimming.


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