I study computational and quantitative biology with a focus on network aging. This site is to serve as my note-book and to effectively communicate with my students and collaborators. Every now and then, a blog may be of interests to other researchers or teachers. Views in this blog are my own. All rights of research results and findings on this blog are reserved. See also http://youtube.com/c/hongqin
Thursday, September 15, 2016
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 . The reads were aligned to the hg19 version of the human genome using the software TopHat v2.0.13 . 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. "