#Bowtie for mac code#
fixed a few typos, cleaning up python code etc.adjusting lower limit for -fusion-multipairs.The user to specify the maximum number of reported fusions in tophat-fusion-post Several fixes/improvements thanks to contributors on GitHub: The default threshold for the inner distance is 250 base pairs this parameter can be set using the -fusion-pair-dist flag.įixed a few issues with GFF parsing of some annotation filesįixed a runtime-error when using -no-discordant option. Pairs with small inner distance (suggesting the pair could come from a plausible pair-end insert) are counted as supporting evidence for the fusion. This algorithm computes the inner distance between read pairs by first converting the pair positions to transcript coordinates using the transcript information in refGene.txt and ensGene.txt. This release implements a new algorithm for counting fusion-supporting read pairs that reduces the number of false-positive potential fusions. TopHat-Fusion algorithm improvements for more sensitive and accurate discovery of fusions, thanks to contributions from Gordon Bean and Ryan Kelley at Illumina. bam2fastx usage message (-h/-help) was updated in order to better document the functions of this program which can be used as a standalone utilityįor converting reads from BAM/SAM to FASTQ/FASTA the -v/-version option was also added to this utility for easier integration in other pipelines.incorporated Luca Venturini's code to support large bowtie2 indexes (.bt2l).improved the detection of linker options for the Boost::Thread library which prevented the TopHat build from source on some systems.TopHat can be now built on more recent Linux distributions with newer GNU C++ (5.x), as the included SeqAn library was finally upgraded to a newer version.Version 2.1.1 is a maintenance release which includes the following changes, some of them thanks to GitHub contributors: spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way. Which provides the same core functionality (i.e. Please note that TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2
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