ArrayExpressHTS – A pipeline for RNA-seq data processing and quality assessment. RNASeq - Wold Lab. Ali Mortazavi, Brian Williams, Kenneth McCue, Lorian Schaeffer, Barbara Wold This is the page of the underlying data and code for the analysis of the paper above, which has been published in Nature Methods in 2008. While the paper focuses on mouse tissues, we have since used the same code in C elegans and human cell lines with great success. If using Bowtie 0.10.X, please make sure to use the new '--strata' flag in order to handle multireads correctly. Note that ERANGE is not compatible with bowtie 0.9.9.X. ERANGE Development Edition ERANGE is now available through Git. Developers wishing to create a clone of the repository can do so using: git clone Experimental BAM support A development version of ERANGE is available from the Git repository.
Important: Discontinue use of ERANGE version 3.2.1 Recently, an error in version 3.2.1 of Erange has emerged that will result in too many peaks being returned by findall.py and a reported FDR that is too high. Help. VCFtools. Picard. Home | Integrative Genomics Viewer. The Genome Analysis Toolkit - GSA. Burrows-Wheeler Aligner. SAMtools. Galaxy.