clean up and tool deprecation

README.md

chipseq_workflow/bowtie2_qc.R

common/enrichemt_notes.md

dge_workflow/RnaSeq_Howto.md

dge_workflow/deprecated/cuffdiff_report.R

dge_workflow/deprecated/cuffdiff_report_NoEnr.R

dge_workflow/deprecated/cutadapt_summary.R

dge_workflow/deprecated/dge_master_template.sh

dge_workflow/deprecated/star_align.sh

dge_workflow/deprecated/topcuff_utils.sh

dge_workflow/deprecated/tophat_qc.R

dge_workflow/dge_howto.md

dge_workflow/dge_utils.sh

dge_workflow/featcounts_deseq_mf.R

dge_workflow/todo.txt

misc/DEPRECATED

misc/fastqc_summary.R

misc/spin.R

misc/spin_utils.sh