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
Bugfixes and stability improvements.
More about this release…
- Get Barnacle for Linux
|1.0.4||Feb 24, 2016||Bugfixes and stability improvements. More about this release…||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. More about this release…||BCCA (academic use)||beta|
|1.0.0||Nov 15, 2012||Initial Barnacle release More about this release…||BCCA (academic use)||final|
|0.1.2||Alpha release More about this release…||BCCA (academic use)||alpha|