RNA-seq pipe update

Automizing for "single end" in RNA_analysis.py
fixing indentations i load_dupRem_20158.py
Chenging make_MarkDup_HT_cuff to ptepare for checking duplication level on higly expressed genes
Insert size ganged in make_tophat_sbatch.py
adding picard insertsixe and top_dup to analysisDB.py