How do I run TopHat2?
Before running Tophat, you have to make an index file that will be used by Tophat. just give any index name (for ex; myindexname). then, in Tophat analysis, for the argument index in Tophat command, just type “myindexname” and run.
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 formats can TopHat results produce?
TopHat produces two output files:
- junctions — A UCSC BED track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction.
- accepted_hits — A list of read alignments in BAM format.
How do I download tophat2?
Download the reference genome Note that bowtie2/tophat2 indices for many commonly used reference genomes can be downloaded directly from http://tophat.cbcb.umd.edu/igenomes.html.
What is HT seq?
HTSeq is a Python package that calculates the number of mapped reads to each gene.
How does bowtie2 alignment work?
Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation.
What is Hisat?
HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments.
Which is the latest version of tophat on GitHub?
TopHat is now available as a public GitHub repository where users are welcome to submit bug reports (issues) and developers are encouraged to submit patches (pull requests). Version 2.0.12 is a maintenance release with the following simple fix: This version is compatible with Bowtie2 v2.2.3.
Why are number of reads incorrectly reported in tophat?
As such, the number of reads with multiple mappings may appear to be incorrectly reported if the user provided options that directly affect the reporting of such multiple mapppings. Fixed a bug that caused TopHat to fail when bowtie1 and pre-filtering options were used together.
How does tophat 2 map against the transcriptome?
TopHat 2 maps reads against transcriptome (optional), genome, and novel/known splice sites using Bowtie 2 (or 1) in a fashion meant to increase the overall mapping sensitivity and accuracy.
How many secondary alignments can tophat 2 report?
In addition to reporting the best (or primary) alignments (the original TopHat behavior), TopHat 2 can report the secondary alignments up to 20 (the default) paired or single alignments (see –report-secondary-alignments and -g/–max-multihits)