RSeQC

[ewels]

Module for RSeQC perhaps?

Edit: This probably isn't a single module, rather a group of several:

• rseqc_inner_distance
• rseqc_geneBody_coverage
• rseqc_read_GC
• rseqc_junctions (junctions_annotation.py and junction_saturation.py together in one module)
• rseqc_read_distribution
• rseqc_read_duplication
• rseqc_tin?

[ewels]

RSeQC needs yet another reference type: a 12-column tab separated, BED plain text file to represent gene models.

Example here and some downloads here

[ewels]

Script to convert gtf to BED12 here:
https://code.google.com/p/ea-utils/source/browse/trunk/clipper/gtf2bed