`view qseq` uses letters `ARND` instead of `ACTG`

Question

`view qseq` uses letters `ARND` instead of `ACTG`

Opened this issue 7 months ago · 5 comments

User diamond version 2.1.7 diamond view --daa ... --outfmt qseq produces sequences that contain the letters ARND instead of ACTG.

When I run diamond --outfmt qseq on the fastq files used to produce the daa file this does not happen. Furthermore the sequences have the same lengths and is a 1 to 1 correspondence between the letters (save a few Ns in the sequences using ACTG), so I don't think they are ambiguity codes.

terrycojones commented 8 days ago

Thanks!

Answer 1 · 2024-04-04T11:30:31.000Z

example.zip
Here is an example running diamond view --outfmt 6 qseq -a this should produce sequences with ARND.

Answer 2 · 2024-04-08T09:30:12.000Z

@bbuchfink Hi Benjamin. Do you have any idea about this issue? I hope you're well! Terry

Answer 3 · 2024-10-21T19:17:28.000Z

It will be fixed in the next release.

Answer 4 · 2024-10-23T03:35:49.000Z

Thank you!