RNA-seq Data Processing


1) bowtie2 manual 
http://computing.bio.cam.ac.uk/local/doc/bowtie2.html
2) bowtie2 download
https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/

3) tophat manual
https://ccb.jhu.edu/software/tophat/manual.shtml
4) tophat download
http://ccb.jhu.edu/software/tophat/downloads/

5) cufflinks manual
http://cole-trapnell-lab.github.io/cufflinks/manual/
6) cufflinks downlad
http://cole-trapnell-lab.github.io/cufflinks/install/


Procedure

1) download all the datafiles into your own directory, then create a new fold \
using "mkdir RNAseq".
There are three files: genome (fasta); RNA (fastq format); Gff3 (annotation)
2) the tools are installed at /home/tools/

How to run bowtie, topHat and Cufflinks

within your own RNAseq directory:

1) /home/tools/bowtie/bowtie2-build genome.fas genome.index
2) /home/tools/topHat/tophat2 genome.index (from step1) RNA.fastq  (fastq RNA-seq file)
	A summary of the alignment counts can be found in ../tophat_out/align_summary.txt
3) using gff as a guide for mapping:
	/home/tools/cufflinks/cufflinks tophat_out/accepted_hits.bam -g annotation.gff3 

if there is no annotaition file, just run as below
	/home/tools/cufflinks/cufflinks ../tophat_out/accepted_hits.bam