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.
How do I run TopHat2?
Tophat2 : Download, build reference genome and align the reads to the reference genome
- Assess sequence quality control with ShortRead.
- Prepare your sample metadata informations.
- Align the reads to reference genome using tophat2.
- Use R to create the list of shell commands :
- Sort and index the BAM files and create SAM files.
What does cufflinks do in RNA-seq?
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts.
What are splice junctions?
Splice-junction sequence signals are strongly conserved structural components of eukaryotic genes. These sequences border exon/intron junctions and aid in the process of removing introns by the RNA splicing machinery.
What is TopHat 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.
How install hisat2 on Linux?
After installing Miniconda (it should automatically add itself to your PATH), you can install hisat2 using the command conda install -c bioconda hisat2 .
How do I create a HISAT2 index?
Create a HISAT2 index HISAT2 can incorporate exons and splice sites into the index file for alignment. First create a splice site file, then an exon file. Finally make the aligner FM index. To learn more about how the HISAT2 indexing strategy is distinct from other next gen aligners refer to the HISAT publication.