1.1 RNA-Seq analysis tools

The table below provides the tools for RNA-Seq analysis that you will use in this tutorial.

Tool	Category	URLs
FASTQC	Home	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
	Program	http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/
	Manual	http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
Trimmomatic	Home	http://www.usadellab.org/cms/?page=trimmomatic
	Program	http://www.usadellab.org/cms/?page=trimmomatic
	Manual	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
Bowtie2	Home	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
	Program	http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/
	Manual	http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
TopHat	Home	https://ccb.jhu.edu/software/tophat/index.shtml
	Program	https://ccb.jhu.edu/software/tophat/manual.shtml
	Manual	https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.tar.gz
Cufflinks	Home	http://cole-trapnell-lab.github.io/cufflinks/
	Program	http://cole-trapnell-lab.github.io/cufflinks/install/
	Manual	http://cole-trapnell-lab.github.io/cufflinks/manual/
STAR	Home	https://github.com/alexdobin/STAR
	Program	https://github.com/alexdobin/STAR/releases
	Manual	https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
BWA	Home	http://bio-bwa.sourceforge.net
	Program	http://sourceforge.net/projects/bio-bwa/files/
	Manual	http://bio-bwa.sourceforge.net/bwa.shtml
Velvet	Home	https://www.ebi.ac.uk/~zerbino/velvet/
	Program	https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
	Manual	https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
Samtools	Home	http://samtools.sourceforge.net
	Program	http://sourceforge.net/projects/samtools/files/
	Manual	http://www.htslib.org/doc/samtools.html
Varscan	Home	http://varscan.sourceforge.net
	Program	http://sourceforge.net/projects/varscan/files/
	Manual	http://varscan.sourceforge.net/using-varscan.html