[Geuvadis_rna_analysis] quantification updates

Hello all, The latest updates on the Geuvadis quantification data front: *Gene, exon and transcript quantifications *- the raw quantification data files of all 667 samples are available as before, unchanged - I changed the library depth normalization from what I uploaded a few days ago - please don't use the old files. - the normalized files now include only the 662 samples that we'll use in analysis *Intron and junction quantifications *- Micha's group has produced the quantifications: intron and junction read counts, and fractions of intron coverage - The available files are - raw gtf files, one per individual - tab-separated tables of the read counts and coverages: raw counts in 667 samples, and library depth normalized counts in 662 samples The directory is /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/quantification/ . See the readmes for details. A word about library depth normalization: before I normalized the exon quantifications by the total number of exonic reads. However, this is not a good correction for intronic reads, and for the sake of consistency I wanted to normalize exon, intron and junction quantifications by the same factor - thus, they are now all normalized by the total number of well mapped reads (mapped, properly paired, MAPQ>150, NM<=6). Have a nice weekend, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch