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@unige.ch