SciLifeLab/scilifelab — pull request #130 by mayabrandi (2012-12-18 10:25:01+00:00)
Title: Develop

analysis_report.py Generates a RNA seq analysis report in rst formate
get_resamp.py Checks for samples with M reads after mapping and dup rem < M ordered
load_dupRem_20158.py Loads 20158 with M reads after mapping and dup rem
make_RseqQc_gbc.py Not in use yet - contains errors
make_sbatch.sh Used by the RNA seq pipeline to generate sbatch scripts
quantify_rRNA.py Makes rRNA raction tabel
RNA_analysis.sh Main script of RNA seq pipeline. Starts the analysis
correl.R Creates FPKM, and count tables. Makes PCA-plot and heatmap
get_stat.py Generates scripts for running bamstat. Part of the RseQC pacage
make_HT_cuff.py Generates scripts for running HT-seq and cufflinks
make_RseqQc_rd.py Generates scripts for checking read distribution - Uses RseqQc pacage
merge.sh Used by teh RNA-seq pipeline to merge several runs
RNA_analysis_delivery.sh To deliver bamfiles, cufflincs outpu, counttable, fpkm-tabel and analysis report.