Heterogeneity Spacers and Primers

[luigallucci]

Hi @marcelm,

thank you for the development of Cutadapt.
I'm actually using the latest stable version and python 3.10.

I'm dealing with these heterogeneity spacers+primers:

Bacterial region V3-V4:
341F (5´-CCTACGGGNGGCWGCAG-3´)
341Fb (5´-TCCTACGGGNGGCWGCAG-3´)
341Fc (5´-ATCCTACGGGNGGCWGCAG-3´)
341Fd (5´-TGTCCTACGGGNGGCWGCAG-3´)
785R (5´-GACTACHVGGGTATCTAATCC-3´)

I would like to know if you know a suggested way to deal with that.
I was thinking to use a file in which I insert these primers (like demultiplexing) but the problem is that basically they are representing the same primers, all equally used on same samples, so I dont need to have 4 different output for each and if I set the files like:

341F
...
341Fb
...
...I feel that this, of course, will lead to different outputs based on the type of primer sequences given, so I'm pretty sure that this is not the right approach.

Do you have suggestions?

[marcelm]

Hi, in case it is still relevant: You can provide multiple primers/adapters with the same name. So something like this:

>341F
(sequence of 341F)
>341F
(sequence of 341Fb)

Then demultiplexing will send them to the same file.

Please leave the issue open as I would like to document this.

[luigallucci]

Hi @marcelm, still useful thank you!

Just a quick question, should be useful also for future people questions...if I'm using just the first one (341F) and not the other, could we consider as they are removed anyway? The structure is 'spacers+primer' where 341F is just 'primer' and the other (b,c,d), instead, have 'spacers+primer'. I was supposing that everything before the 'primer' is removed.