Colin Diesh

You can hover over the location bar to get coordinate this way  I know that igv has some per-base hovering that jbrowse does not have however, is that what...

Is your data paired-end and stranded? I know it's possible to have single end stranded too, and in that case, it should display fine without the new options in 1.11.6....

The 'useXS' and 'useReverseTemplate' should take care of extra "biological" cases of strand display. These can also be enabled via the user interface track menu for easy usability. To describe...

Screenshots previously in this thread show both cases

There will be a new BAM tag called TS that can indicate strand of reads https://github.com/samtools/hts-specs/issues/276 This is basically identical to XS:A which is a custom field used by tophat...

I am incorporating the suggestion to make those options say "RNA-seq orientation" in my paired read branch

Technically this issue arises on desktop too, probably just exageratted on mobile :) It would be interesting if you could "side scroll" the faceted columns if I am imagining correctly

@FredericBGA You can potentially use the system of "includes" and include private tracks in a different privateTracks.json and then add "include": ["privateTracks.json"] http://gmod.org/wiki/JBrowse_Configuration_Guide#General_configuration_options Then only the authorized user would have...

You might also consider BigBed format which keeps all info on the same line. The gtf2bed script https://github.com/dasmoth/gtf2bed and this PR can go some ways towards accomplishing this https://github.com/GMOD/jbrowse/pull/944

It's not necessarily true that BED file doesn't allow arbitrary key value pairs. The bed file "autosql" concept allows arbitrary information encoding, and this can be converted from other formats...