What does RNA star do?

In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates providing scalability for emerging sequencing technologies.

What is star in RNA-seq?

Spliced Transcripts Alignment to a Reference (STAR) is a fast RNA-seq read mapper, with support for splice-junction and fusion read detection. STAR aligns reads by finding the Maximal Mappable Prefix (MMP) hits between reads (or read pairs) and the genome, using a Suffix Array index.

What is TopHat2?

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 Star aligner?

STAR is by far the fastest RNA sequence aligner. It was developed by Alexander Tobin and coworkers in 2012. It can detect canonical and non-canonical splice junctions and fusion transcripts with or without reference annotation. It can also map full-length RNA sequences.

What is sjdbOverhang?

The –sjdbOverhang is used only at the genome generation step, and tells STAR how many bases to concatenate from donor and acceptor sides of the junctions. If you have 100b reads, the ideal value of –sjdbOverhang is 99, which allows the 100b read to map 99b on one side, 1b on the other side.

Is Star splice aware?

The alignment process consists of choosing an appropriate reference genome to map our reads against and performing the read alignment using one of several splice-aware alignment tools such as STAR or HISAT2.

How do I install tophat2?

Building TopHat

  1. Unpack the TopHat source tarball: tar zxvf tophat-2.0.0.tar.gz.
  2. Change to the TopHat directory: cd tophat-2.0.0.
  3. Configure TopHat using the ./configure script.
  4. Finally, make and install TopHat.

What is FPKM value?

FPKM stands for fragments per kilobase of exon per million mapped fragments. It is analogous to RPKM and is used specifically in paired-end RNA-seq experiments [17].