Marcel Martin

You’re using an older Cutadapt version - please update!

I’m not saying we have to do this but want to document what I found. There’s also [`PyUnicode_GetLength`](https://docs.python.org/3/c-api/unicode.html#c.PyUnicode_GetLength), which is in the stable ABI. It’s not a macro, so it’ll...

A stable ABI will likely come with Python 3.15, see [PEP 803](https://peps.python.org/pep-0803/). The cool thing is that the wheels would then work with both the GIL-enabled Python and the free-threaded...

Without more context, I don’t know how to run it in this particular case. I may be able to help if you post an example read and the command that...

Hi, (a small ask for next time: Please avoid posting screenshots of terminal output, and paste the actual text instead. This makes it easier for me to read and to...

You should be able to use a [non-internal 5' adapter](https://cutadapt.readthedocs.io/en/stable/guide.html#non-internal) instead of an anchored 5' adapter, and then require that the minimum overlap is 4. For example, if your barcode...

> However, I found I got many reads (around 90%) in unknown-unknown.fastq.gz Ok, maybe I misunderstood: In your first message, you said "many barcodes in my data is shorter than...

You could try discarding all reads shorter than 50 bp using `--minimum-length=50`. That should get rid of all poly-A-trimmed reads.

Yeah, this is actually the only way to do this at the moment. Note that you can omit `--no-indels` and simply ignore the warning; there shouldn’t be any downsides to...

Maybe helpful as a start: The KeyError crash is fixed in Cutadapt 5.1, which I just released.