RNAseq analysis protocol

"Quality of the reads was analyzed with FastQC v0.10.1, and trimming of low-quality reads was performed with Trimmomatic v0.33 [1]. The reads were aligned to the hg19 version of the human genome using the software TopHat v2.0.13 [2]. The Human UCSC hg19 genome annotation was downloaded from Illumina’s FTP repository located on ftp://igenome:G3nom3s4u@ussdftp.

illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz. Expression quantification was obtained with CuffLinks v2.2.1, CuffMerge v1.0.0 and CuffDiff v2.2.1. " 

=> FASTQC
http://www.bioinformatics.babraham.ac.uk/projects/download.html


=> Trimmomatic v0.33

=> hg19 from UCSC

=> TopHat

=> Expression quantification CuffLinks v2.2.1, CuffMerge v1.0.0 and CuffDiff v2.2.1.