ChimPipe.0.9.8

The extraction of reads to remap is made simpler with a single samtools fastq command

ChimPipe v0.9.7

Extraction of reads to remap after 1st mapping step is done with samtools rather than bedtools
Need to use bedtools version at least 2.29.0

ChimPipe v0.9.6

This release essentially corrects the samtools sort command (new way of specifying arguments)

ChimPipe version 0.9.5

New Features

• Added converters of ChimeraScan, CRAC, FusionMap, PRADA and TopHat-Fusion outputs into ChimPipe format .
• New tool for annotating chimeric junctions according to the chromomal position of their donor and acceptor sites.

ChimPipe version 0.9.4

Bug fixes

• Check gene_id instead of gene_name to decide associating a gene to the exon.
  gene_name info not always available leading to problems.
• Replace gff by bed files for intersecting aligments with the annotated exons. Bed files are better supported by bedtool developers than gff.

Documentation

• Documentation update
• Chimpipe 0.9.4 manual pdf

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.

ChimPipe version 0.9.1

New features

• Multimapped split-reads considered for chimera detection.
• New ChimPE module. Search for consistent paired-end supporting the existence of each chimeric junction. Chimeric junctions do not supported by at least one consistent paired-end will be discarded in the filtering module as false positives.
• New ChimFilter module. Improves ChimPipe precision by filtering chimeric junctions according to 8 different criteria (number of spanning reads, consistent pairs, novel splice-sites, gene homology..). Completely tunable.
• New output file containing the filtered chimeric junctions and the reason why they were filtered out.
• Additional pieces of information provided for each chimeric junction (number of consistent paired-end, supporting reads identifier ...).

Bug fixes

• Fixed problem in ChimSplice. Coordinates went into over the chromosome limits and the script failed, added an upper and lower bound.

ChimPipe version 0.8.8

New features

• Pipeline able to take a bam file as input. Now it has two running modes: FASTQ and BAM as input.
• Modifications in the way to run the pipeline and in the output directory structure to make it more flexible, clear and avoid some problems.
• Pipeline configuration displayed in a clearer way.
• Decreased the false positive rate. Remap only those multi-mappings with more than 10 hits instead of all the multi-mappings. This was leading to some false positives arising from alignment artifacts.

Bug fixes

• Fixed a bug when an output directory is specified. Wrote in the cwd instead of the desired directory.
• Fixed a problem in the step to extract mappings to remap in the second mapping phase. Missed alignments with 5 edit distance.
• Fixed problem with reads split-mapping without canonical splice sites. Program was producing wrong formatted chimeras file.