Jbrowse: importance of draw-basepair-track.pl
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6.4 years ago
CikLa ▴ 90

Hi,

I found a script named draw-basepair-track.pl in JBrowse program. May I know, what is that actually? Why do people want to draw the basepair track, is there any need of it? Just curious to know.

Regards,

CikAlal

jbrowse genome browser Forum • 2.1k views
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6.4 years ago
cmdcolin ★ 1.5k

It is a fairly old feature, but it still works. The functionality is documented here http://gmod.org/wiki/JBrowse_Configuration_Guide#draw-basepair-track.pl

 

There is also an example file "tests/data/base_pairing/XdecoderStructure.gff" on github that you can test out, see https://github.com/GMOD/jbrowse/tree/master/tests/data/base_pairing

Loading script

bin/prepare-refseqs.pl --fasta tests/data/base_pairing/mahoney.fa
bin/draw-basepair-track.pl --gff tests/data/base_pairing/XdecoderStructure.gff

(must have GD::Image perl installed)

 

Example base pairing track

 

 

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note for future generations you might consider the sashimiplot plugin https://github.com/elsiklab/sashimiplot/ it renders arcs in JS instead of pre-rendering to disk with libgd

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6.4 years ago
Mitch Skinner ▴ 660

The original motivating application was to show patterns of base pairing in RNA secondary structures.

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