A pipeline for detecting and characterizing chimeric transcripts from long RNA sequences, such as those generated by de novo transcriptome assembly. It identifies sequences with a variety of anomalous alignment topologies, predicts partial tandem duplications (PTDs), internal tandem duplications (ITDS), and fusions from these sequences, and measures the coverage of the inferred chimeric transcripts relative to corresponding wild-type transcripts.
The Barnacle pipeline is composed of five stages:
Stage 1) Examine contig-to-genome alignments and identify anomalous or non-reference (candidate) contigs that have a variety of alignment topologies,
Stage 2) Examine transcriptome read alignments to assembled contig sequences and calculate read support for these candidate contigs,
Stage 3) Apply user-specified filters to the candidate contigs and retain only sufficiently confident candidates,
Stage 4) Identify chimeric transcripts of particular types (PTDs, ITDs, and fusions) from the filtered candidates,
Stage 5) Compare the coverage of the predicted chimeric transcripts to their corresponding wild-type transcripts.
Released Feb 24, 2016
This update fixes several bugs encountered while parsing SAM files as well as when annotating predictions with genes. It also adds a rudimentary output parser for generating targeted reports and a 'robust' mode to allow Barnacle to skip problematic contigs and keep running on the rest of the input data.
Major changes since version 1.0.3
- Fix several bugs in the parser for SAM-formatted contig-to-genome alignment files
- Fix a bug in the code for annotating predictions with gene names
- Fix a bug in the read-to-contig support calculator for when no read support is found for any events
- Add rudimentary output parser for creating targeted ITD reports
- Add 'robust' mode to allow Barnacle to skip problematic contigs and keep running on the rest of the input data
|1.0.4||Feb 24, 2016||Bugfixes and stability improvements.||BCCA (academic use)||final|
|1.0.3||Update to increase compatibility with newer versions of Trans-ABySS (1.4.x), primarily allowing SAM-formatted contig-to-genome alignment files, and improvements to ITD detection.||BCCA (academic use)||beta|
|1.0.0||Nov 15, 2012||Initial Barnacle release||BCCA (academic use)||final|
|0.1.2||Alpha release||BCCA (academic use)||alpha|