how to visualize arcs in higlass

[higlass]

how to visualize arcs in higlass

[vivekbhr]

I thought of importing it as bedpe file like:

clodius aggregate bedpe --assembly mm10  --chr1-col 1 --from1-col 2 --to1-col 3   --chr2-col 4 --from2-col 5 --to2-col 6 --output-file /tmp/test.arcs

followed by:

sudo higlass-manage ingest --filetype beddb --datatype bedlike /tmp/test.arcs

but I couldn't see anything.. I would try bedfile now

[vivekbhr]

Ok, I'll play around with it. Thanks a lot for the fast replies! The tool is amazing

[pkerpedjiev]

Hey Vivek,

The arcs track is still a bit experimental so it's not easy to add. But it is possible.

If you use the latest docker container and you ingest your data with --filetype beddb --datatype bedlike. Add your data as a bedlike track from the Add Track Dialog. Once it's loaded, open the the viewconf editor:

Scroll down to the section for your track (look for type:bedlike). Change that to type: 1d-arcs and delete the uid:... section for that track. Save the viewconf and you should be able to see the arcs track.

We'll improve that process and make it easier to add as a track shortly.

[vivekbhr]

thanks @pkerpedjiev . Do I need to run clodius aggregate first?

[pkerpedjiev]

Yes, you need to run clodius aggregate bedfile on the bedfile and then ingest the resulting beddb file using --filetype beddb --datatype bedlike.

[vivekbhr]

I am still unable to see the arcs. I can see the individual positions though.

Does this need any update? Here's what I have in higlass-app/version.txt

SERVER_VERSION: 1.14.1
WEB_APP_VERSION: 1.1.8
LIBRARY_VERSION: 1.9.3
HIPILER_VERSION: 1.4.0
MULTIVEC_VERSION: 0.2.3
CLODIUS_VERSION: 0.14.3
TIME_INTERVAL_TRACK_VERSION: 0.2.0-rc.2
LINEAR_LABELS_TRACK: 0.1.6
LABELLED_POINTS_TRACK: 0.1.12
BEDLIKE_TRIANGLES_TRACK_VERSION: 0.1.2
RANGE_TRACK_VERSION: 0.1.1
PILEUP_VERSION: 0.2.11

[pkerpedjiev]

I think they're there. Just zoom in to one of the bars on the top :-)

[vivekbhr]

@pkerpedjiev oh yes I see them now! I think I was expecting some over longer distances. My bad!

Are, there any limitations in visualizing one-to-many kind of connections?

[pkerpedjiev]

Hmm, I haven't tried out one to many. It shouldn't be a problem if you have multiple bed lines:

chr1 1000 3000
chr1 1000 5000