Marcel Martin
Marcel Martin
It’s been a while since this issue has been opened, and while this is an interesting idea, realistically, I don’t see us implementing this anytime soon. So I would like...
Hi, the `Xfile:` syntax is not supported at the moment (see https://github.com/marcelm/cutadapt/issues/361). You would need to manually add the `X` to each sequence in your `fwd.primers.fasta` file instead. That said,...
Can you clarify what you mean by "disambiguated FASTA file"? In which way are the primers degenerate? Note that adapter/primer sequences can contain IUPAC wildcards, maybe that helps?
I’ve recently dealt with an issue in strobealign that made me a bit more sensitive to the relative overhead introduced by using compressed files. It turned out that decompressing (not...
Oh, interesting, I guess this needs to be done on the bgzip-level?
Awesome, thanks! Will hopefully be able to review this towards the end of the week, no time today.
Feel free to merge when ready.
For 1.8.0, PyPy wheels are missing on PyPI. They were still provided for 1.7.2. See also https://github.com/pycompression/xopen/pull/173 .
I ran a small experiment on our fruit fly test and CHM13 datasets where I used different `-r` settings to map reads of different actual lengths. The current stable release...
Hi, there’s a [section in the documentation](https://cutadapt.readthedocs.io/en/stable/recipes.html#trimming-amplicon-primers-from-paired-end-reads) about this. You don’t need the `--pair-filter` option. This is only relevant when you use an option that filters the reads such as...