ns auxillary field is already set for ONT sequencing by dorado

[owensnick]

You may already be aware, but Nanopore uses the ns:i as a tag:
https://software-docs.nanoporetech.com/dorado/latest/basecaller/sam_spec/?h=ns#read-tags

This tag is the set to nucleosome positions by fibertools.

It would be great if alternative tag names could be set as an option in fibertools, perhaps set in the header, for automatic identification of files that use a different convention.

[mrvollger]

That's very good to know and something I was trying to avoid but apparently failed.

We are working on a:
https://github.com/fiberseq/Molecular-annotation-spec

This will replace all the fiber-seq tags in the future. But I am unlikely to have time to make a workaround in the meantime.

I am going to leave this open as an FYI to others and a note that this new spec is in the works.

Thanks,
Mitchell

[sathish-t]

I would support this draft tag as well. We in the Nieduszynski group work on measuring aspects of DNA replication using long-read sequencing and our work involves annotating tracks on single molecules based on BrdU signal. I can imagine us doing MA:Z:left_fork and the like if such a tag is implemented.

[mrvollger]

Very good to hear! Perhaps i can make a draft implementation over the break.

It would be great if you could voice your general support here as well:

samtools/hts-specs#846