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

bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.

GNU General Public License v3.0

992 stars 182 forks source link

`view qseq` uses letters `ARND` instead of `ACTG` #798

Open imLew opened 3 months ago

imLew commented 3 months ago

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.

imLew commented 2 months ago

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

terrycojones commented 2 months ago

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