ChimPipe version 0.9.3

New features

• Chimeric junctions classified in one of these 5 categories: readthrough, intrachromosomal, inverted, interstrand and inter chromosomal.
• Maximum number of accepted mismatches for the first mapping dependent on the read-pair length (4%).
• New biotype filter. It filters out junctions involving genes in a black list. Default gencode 19 human pseudogenes.
• Refinement in default filtering configuration to improve sensitivity and precision.
• ChimSplice. Exons and junctions required to be in the same strand to report overlap.

Documentation

• Update
• New tutorial describing how to use ChimPipe to rediscover 5 fusion genes in a cancer cell line.

Bug fixes

• Problem with biotype filtering. List of filtering reasons contained duplicated or even triplicated biotype tags.
• Wrongly formatted header in the middle of the chimeric junctions output file.