Monday, 9 January 2012

TopHat 1.4.0

TopHat 1.4.0 release 1/5/2012

Version 1.4.0 includes the following new features and fixes:

when a set of known transcripts is provided (-G/--GTF option) Tophat now takes the approach of mapping the reads on the transcriptome first, with only the unmapped reads being further aligned to the whole genome and going through the novel junction discovery process like before. This new approach was implemented by Harold Pimentel.
new command line options have been added for the new mapping-to-transcriptome approach; please check their documentation which includes important notes about the new --transcriptome-index option for efficient use of this approach
the unmapped reads are now reported in the output directory as unmapped_left.fq.z (and unmapped_right.fq.z for paired reads)
the --initial-read-mismatches value now also applies to final alignments resulted from joining segment mappings
we adjusted the selection of hits to be reported in case of multi-mapped segments, reads and read pairs
enhancements in junction discovery for the segment-search method in the case of paired-end reads
the reported running time now includes days
fixed the non-deterministic behavior that could cause some differences in the output of repeated Tophat runs
fixed a regression bug that prevented the use of SOLiD reads with certain length of quality values

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