N and H nucleotides in V3-V4 primers and cutadapt trimming

Technical Support
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1

I hope I didn’t missed any post about V3_V4, but I couldn’t find an answer:

Here is the V3-V4 forward and reverse primers:
Forward CCTACGGGNGGCWGCAG
Reverse GACTACHVGGGTATCTAATCC

It is a quick technical question, do you think that trimming primers (I am using cutadapt in this case) which have "N" and "H" nucleotides should work? these nucleotides are not any of specific nucleotide (ACGT).

Thank you
Marwa

2

Hello!
As it is stated in the plugin description, those letters in sequences can be handled with the following flags

--p-match-read-wildcards / --p-no-match-read-wildcards
Interpret IUPAC wildcards (e.g., N) in reads.
[default: False]
--p-match-adapter-wildcards / --p-no-match-adapter-wildcards
Interpret IUPAC wildcards (e.g., N) in adapters.
[default: True]

In your case wildcards in the primers, so plugin should handle them by default.
Hope that this will help

Best,

3 Likes
3

Sorry missed that point in the description @timanix
it is a bit strange as I ran without and I found primers found. Do you know why this happens?

4

Probably because:

So it will work in primers by default:

1 Like
5

Sorry, you mean default in cutadapt or in qiime2?
I mean I got primers although I didn't run wildcards. So this means that cutadapt has adjustment without the need to add the wildcards. I am asking as I am lazy to run my analysis again I have already done.

6

Yeap! In qiime2.
In future, please read the plugin description before posting. It is written there.

7

sorry I did in older version of qiime that is why.
it seems that is also default in cutadapt outside qiime2 becasue I have ran this part of analysis aslo in R

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