TopHAT 2.2

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology.
Features:
- Quality value strings beginning or ending with "*" are no longer truncated to a single quality value "*" in accepted_hits.bam
- SOLiD reads that have "!" (or 0) as the first quality value caused a runtime error, which is now fixed
- closure-search is compatible with internal file compression
- max-deletion-length option is correctly handle
A new option --initial-read-mismatch option is introduced that users specify the number of mismatches allowed in the initial read mapping
- For short reads (usually <45-bp), it is recommended that users decrease segment length (--segment-length) to about half the read length and segment mismatches (--segment-mismatches) to 0 or 1