This is a partial list from a larger set whose composition is always evolving. The best choice of software tools and running parameter choices depends on the aims of the study and on specific data properties. Consulting about the analysis path is best begun at the design stage of a study.
- SOM Viewer This is an interactive tool for visualizing and mining the ENCODE chromatin Self-Organized Map (SOM) (Nature, 2012, in press). It allows a user to see the overlay of many other data-types onto this SOM and to mine the content of SOM units or user specified clusters of units.
We manage the local Caltech installation of the UCSC Genome browser. It is customized for Caltech labs, providing rapid access to private collections of data for projects in progress plus other high-value data-sets imported by Caltech labs for their routine use. This is an interactive website offering access to genome sequence data from Caltech-requested vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.
Access to the genome browser is available by contacting Henry Amrhein
Once you have an account to access the server, you can follow the instructions to load custom tracks, or the tracks can be loaded by Henry Amrhein.
- Cufflinks was the first software package to take on the problem of assembling novel transcript models and then estimating their abundance in one or more RNA-seq datasets. It accepts aligned RNA-seq reads and assembles the alignments into a parsimonious set of transcript models. It then estimates the relative abundance of these transcript species based on how many reads support each one. A series of newer Cufflinks versions since the original release have significantly improved it, although it remains sensitive to details of use and to specific data structure.
ERANGE: A package of Python scripts designed for very basic analysis of high-throughput sequence data from the Illumina platform for RNA-seq and ChIP-seq in metazoan genomes. The original RNA-seq portion of ERANGE was described in the Nature Methods paper "Mapping and quantifying mammalian transcriptomes by RNA-seq" (Mortazavi, 2008), and the original ChIP-seq peak caller was first described in Johnson* and Mortazavi* et al., (2007).