Very Lightweight And Fast Genomic Bed Viewer

Question

[Gabriel R.]

I deal a lot with bed files on hg19. Is there a very lightweight, no fuss, very fast viewer to do:

./viewer [bed file in] [pdf file out]

and you could view distribution of the ranges in the pdf file similar to something like this: http://cistrome.dfci.harvard.edu/CaSNP/gscore/ I do not want to open a graphical user interface for a genome browser each time I apply a tiny little filter.

[Ryan Dale]

What do you mean by "distribution of ranges"? A histogram of feature sizes? Or each line in the BED file placed on a chromosome? Can you give an example of what you want to have in the PDF?

[Gabriel R.]

something simple along those lines :http://cistrome.dfci.harvard.edu/CaSNP/gscore/

[Ryan Dale]

Have you tried the answers at Drawing chromosome ideogams with data? In particular, the second plot in this answer: A: Drawing chromosome ideogams with data

[Gabriel R.]

They are all R packages, hasn't someone build either a wrapper or something faster and easier to use ?

Answer 1

[Istvan Albert]

what you could do is use something like Casper JS to load into a headless browser that can also screenshot anything.

The bonus is that you can use commonly used websites, navigate the pages and do all sorts of fancy things