Marcel Martin

How many barcodes are in `barcodes_fwd.fasta` and `barcodes_rev.fasta`, respectively? Are you sure you have combinatorial dual indices? According to [Illumina’s documentation](https://knowledge.illumina.com/library-preparation/general/library-preparation-general-reference_material-list/000002344), you can have up to 96 samples, so I...

I still don’t have a clear picture of how your data is structured. I believe you need to understand this yourself before you can proceed. In particular, you need to...

> What is the correct combination of fastq.gz files for further analysis? I have a total of 230 samples. > How can I pick those right files from the combination...

Yeah, I saw that, but it is quite low on my to-do list. I’ll try to get this done for the next release.

dnaio PR: https://github.com/marcelm/dnaio/pull/134

> After running the pipeline until round 2, then reversing the files and processing everything again...do I have to merge the resulting files via the cat command? Yes, I forgot...

> I just added `0=99` removing `^` at the beginning. Just a simple check before looking into this any further: Did you enclose the text in quotation marks? Otherwise, the...

Thanks, this is interesting. I’ll have to think about whether I want this. I agree the code is not that intrusive, but it would require some documentation and may cause...

> The latest version of [dnaio](https://github.com/marcelm/dnaio) (the library that cutadapt uses for sequence IO) has uBAM read support. So cutadapt can already read uBAM files. To clarify: Only single-end reads...

Good idea, but I’ll need to think about how to do this the best way. Because the adapter trimming statistics would change, it is a backwards-incompatible change.