from RPubs by Alex Chitsazan
This is a script that will do differential gene expression (DGE) analysis for RNA-seq experiments using the bioconductor package edgeR.
To give background on this project, this is a RNA-seq project that is being done in planarian, Schmidtea mediterranea, a flatworm that has remarkable regeneration properties. This project is being done in the lab of Alejandro Sanchez Alvarado, an HHMI funded lab at Stowers Institute for Medical Research. More knowledge of the lab and of planaria can be found here. The primary biochemical research is being done by a postdoc, while all bioinformatics and NGS analysis was done by myself, Alex Chitsazan.
This project is an RNA-seq experiment being done to look at the differential gene expression levels of an RNAi knockdown of the methyltransferace mll, compared to an RNAi control, unc, looking at the whole worm (WW). This was done at three time points, day 9, 12 and 15 after RNAi exposure. As stated above, DGE analysis was done using the bioconductor package edgeR.