Marcel Martin

The difference between `-a` and `-g` for linked adapters lies in which adapters are required to be in the read, see https://cutadapt.readthedocs.io/en/stable/guide.html#linked-override . For `-g`, both adapters are required. For...

To require the full barcode to be present, use an [anchored adapter](https://cutadapt.readthedocs.io/en/stable/guide.html#anchored-5adapters). You can either add the `^` to each sequence in the FASTA file: ``` >HL001_FW ^ATCCGGTCGGAGA...TCTCCGACCGGAT ``` or,...

> In the forward read (R1) I still find a few Fwd primer sequences, as well as I find a few Rev primer sequences in the R2 reads. **Is this...

> R1 and R2 reads have already been merged into each sample file). You say "merged", but also mention "interleaved", however, these are two different things, so I’m not sure...

I’m sure this is just an issue in your script. Some ideas for debugging: - Add `echo` before `cutadapt` in your command. This will print out the commands that would...

You would probably have to use the [`--info-file` option](https://cutadapt.readthedocs.io/en/stable/reference.html#info-file-format) and postprocess the generated file. Ideally, would you want Cutadapt be able to split a read into two?

> Hello, I have a few questions and observations about the behaviour of the --revcomb flag for when cutting off primers from paired-end data. > > 1. Using a single-read...

I've now been able to reproduce the problem on Windows 10. I can also see where the function is called twice, will see what I can do.

Interesting, it works on Python 3.10, 3.11 and 3.12.0, but fails on 3.12.4. Bisecting points to commit https://github.com/python/cpython/commit/de347c02070f7b1e8a4810ece5e898b22b4070cd (part of 3.12.3).

I realize only now that this is the same issue as the one that we encountered in dnaio two days ago when trying to make a new release. This is...