Request- add location of telomeres?

[desmodus1984]

Hi,
My group assembled a genome using PacBio Hifi and then scaffolded using Hi-C.
I was wondering if it would be possible to add the location of telomeric repeats to the graph/figure to identify "canonical/complete" chromosomes, and identify also A and B chromosomes.

Thank you

[JustinChu]

HI @desmodus1984. Sorry for the late reply, I've started a job in industry and have been quite preoccupied by that.

Perhaps a general option for including a bed file with labels to mark with a custom colour might be best, similar to how gaps are rendered.

Then perhaps you could run I can think of a general fast motif finding maybe teloscope?

Any thoughts on this?

[desmodus1984]

Hi.
Congratulations on your industry job.
That's a great idea. Thank you for pointing that up.
I wanted to ask one last question. I used the following code for plotting the genomes:

jupiter name="no-cut.${PBS_JOBNAME}-JC" fa=Lepwed.softmasked.fasta ref=NSch.chr.fasta t=64 labels=both \
        maxGap=200000 maxScaff=36 MAPQ=55 ng=99 m=5000000 minBundleSize=100000

Oddly, for the Lepwed genome some labels are off margin, and cut half-way.

Is it possible to increase the margins or reduce the plot so that the labels are shown complete in the figure?
Thank you very much;

[JustinChu]

Is it possible to increase the margins or reduce the plot so that the labels are shown complete in the figure? Thank you very much;

Sorry is a bit cumbersum but the the raw config in /jupiterplot/config/rawConf.conf or on the prefix.conf file produced by the pipeline can be changed in here which can adjust this. See this comment: #47 (comment)

Since this a common question maybe it would make sense for it to be a configuration parameter...