Jared Simpson

There's really no explanation other than the index files are missing. Can you show me an `ls` of the directory and what command you tried to run?

I agree this is confusing. I propose to get rid of the `--aligned` and `--unaligned` options, since they are the default behaviour. The options will be `--no-aligned` and `--no-unaligned`, which...

Can you post the first hundred lines or so of the bam file with `samtools view`?

I strongly recommend that if you add support for MinION data you only wrap the `artic` commands from the [SOP](https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html) in the same style as the [nextflow wrapper](https://github.com/connor-lab/ncov2019-artic-nf/blob/master/workflows/articNcovNanopore.nf). There's been...

Thanks for the early feedback @adbeggs. I don't think Bioperl specifically needs to be installed but openssl does seem to need some perl libraries. I'll look into this more and...

Thanks for the fast reply. The genome I am working on is quite large, but I may try v0.2.5 anyway. Please do let me know when this is re-implemented and...

The polyA module is only for direct RNA sequencing, not DNA, so it doesn't work with any of the DNA chemistries (R9.4, or R10.4). Since poly-A calling is now available...

No, you should use dorado for RNA004On Sep 4, 2024, at 1:03 PM, bnpapas ***@***.***> wrote: Yes, though it is partly my fault for not having a good handle on...

Hi, The read_index is over the alignments in the input bam file, so you may be able to get the read_id from it. Jared

This issue and #744 is very useful for an assembly I am working on. I am unclear about the `-5` (genetic map) option, is there documentation about what the file...