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fDesc[0] = "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. <br /> Features:<br /> - Quality value strings beginning or ending with &quot;*&quot; are no longer truncated to a single quality value &quot;*&quot; in accepted_hits.bam<br /> - SOLiD reads that have &quot;!&quot; (or 0) as the first quality value caused a runtime error, which is now fixed<br /> - closure-search is compatible with internal file compression<br /> - max-deletion-length option is correctly handle<br /> A new option --initial-read-mismatch option is introduced that users specify the number of mismatches allowed in the initial read mapping<br /> - For short reads (usually &lt;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";

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