how to trim spacers without trimming primers

I have paired End data, for which have done adaptor trimming.
I want to trim few base spacers present at 5’ end of a primer. This primer is commonly present in all reads R1, but the spacers are of different base composition and different length. Can I specifically trim these spacers which are present at 5’ end of primer without trimming the primer sequence??
Eg Primer Sequence is GACTACGTTGAG
Primer sequence along with Spacer are ATA GACTACGTTGAGC
I Want to trim these spacer sequence but no the primer sequence. Can you please guide how should I do it. Same way for R2 reads only the primer sequence and spacer is different.

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Hi @Malen,

Why not trim the primer sequence? In general, trimming primer sequences is recommended prior to denoising or OTU clustering. The primer sequences will be very highly conserved so is generally not useful, e.g., for phylogeny or taxonomy classification.

Moreover, trimming the primers would make this easiest: use QIIME 2’s q2-cutadapt plugin to trim the primers (and everything to the 5’ end of each primer, i.e., the spacers that are giving you trouble).

Another alternative is to import the raw data into QIIME 2, i.e., before any adapters have been trimmed, and use q2-cutadapt to trim the adapters+spacers (you would run it three times, once for each adapter + spacer combination).

Good luck!


Hi, Thanks for the reply. But a spefically want to cut the spacer and not the Primer. Can you please help me to perform it.

I already offered a suggestion above:

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