Trick : seqMINER

seqMINER is a Chip-seq density clustering and plotting software. A trick to keep clustering from previous computations and plot the same ordering on a new set of bam/bed files: Load your bam file, right click and choose view heatmap (bypassing the "cluster" button). Voila!

MISO sashimi plot (RNA-seq alternative splicing)

This is a modified python script from the MISO package for plotting alternative splicing events.

Modifications from the source:
1) Normalized junction counts (assumming that the junction reads are proportional to total read coverage)
2) Proper plotting of isoforms (lines do not extend beyond final exon/utr if one isoform is shorter than the other)