Tophat2
TopHat is a fast splice junction mapper for RNA-Seq reads.
Tophat2. 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 popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat.
Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. It first aligns RNA-Seq reads to reference genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
It's 50 for uniquely mapped, and then 0-3 for various degrees of multiple mapping. TopHat/TopHat2 TopHat is a fast splice junction mapper for RNA-Seq data. Your results are normal, the MAPQ scores reported by tophat2 are not related to -10*log10 (probability the mapping is wrong).
TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. Abstract TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. Spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way.
ADD COMMENT • link written 6.6 years ago by Devon Ryan ♦ 96k 3. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat 2.1.1 release 2/23/16 Please note that TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality (i.e.
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