What does TopHat2 do?

TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat.

What is TopHat in RNA-seq?

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.

What is genetic alignment?

Sequence alignment is a way of arranging protein (or DNA) sequences to identify regions of similarity that may be a consequence of evolutionary relationships between the sequences.

How does tophat work to map the reference genome?

TopHat will map your reads first by running Bowtie to identify places where reads map end to end. Since your reads came from spliced transcripts in an RNA-Seq experiment, Bowtie will identify “islands” in your reference genomewhere reads piled up.

What is the purpose of the tophat program?

TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.

How to install Tophat in TopHat2 wrapper?

The tophat2 wrapper makes sure that the local execution PATH gives priority to the new binaries and it should not interfere with the TopHat programs from the previous installation. Finally, make and install TopHat. This will install tophat and its modules into /path/to/tophat_base_dir/bin directory.

How is TopHat2 used to align transcripts?

In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes.