Flow Documentation

Partek Flow Documentation

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Numbered figure captions
SubtitleTextFusion attribute report of TopHat-Fusion fusion gene detection algorithm. Each row represents a fusion gene candidate (the example shows comparison of number of fusion reads detected in ER– group vs. ER+ group, with the p-value based on χ2 test)
AnchorNameFusion attribute report

STAR Algorithm

General Overview

STAR aligner (see Chapter 6.1) also has the ability to detect fusion genes (referred to as “chimeric alignments”) (5). During the first phase of alignment, STAR searches for maximal mappable prefixes (seeds) of sequencing reads. In the second phase, all the seeds that align within user-defined genomic windows are stitched together. If an alignment within one genomic window does not cover the entire read sequence, STAR will try to find two or more windows that cover the entire read. This essentially results in detection of fusion events, with different parts of reads aligning to distal genomic locations, or different chromosomes, or different strands.

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