## Gene Quantification (for RNA-Seq libraries) was performed by using the output of STAR aligner (Bam files) as input for Cuffquant. The cuffquant output for all the libraries was used as an input for cuffnorm.

## GTF files were downloaded from UCSC using: genePredToGtf mm9 refFlat mm9.gtf (for mouse) or genePredToGtf hg19 refFlat hg19.gtf (For Human).

## Fasta Files used in Cuffquant resulted from merging of the Canonical Chromosomal Fasta files used for the creation of the STAR genome Indices.

## Script Gene Quantification using Cuffquant:

cuffquant -o /Path/To/Output/ -u -p 10 --library-type fr-unstranded -b /Path/To/Merged/Fasta/File.fa /Path/To/GTF/File.gtf /Path/To/Mapped/Library.bam


## Script for normalizing the Expression values to FPKM using cuffnorm:

cuffnorm -o /Path/To/Output/ -L Labels,for,libraries -p 10 --library-norm-method classic-fpkm --library-type fr-unstranded /Path/To/GTF/File.gtf /Path/To/Library1.cxb /Path/To/Library2.cxb..../Path/To/Library(n).cxb 


