Update code for protein coding genes tss.

excluded_regions_processing.sh

 # Make a universe of excluded regions of the genome
+cd MakeGencodeTSS
+./make_TSS_file_from_annotation_with_confidence_better.sh ../gencode.v19.annotation.gtf ../biotypes.txt
+gtf2bed  < MakeGencodeTSS/gencode.v19.annotation_capped_sites.gff > gencode.v19.annotation_capped_sites.bed
 
 ## Gencode Protein Coding genes
 bedtools slop -i gencode.v19.annotation_capped_sites.bed -g hg19.chrom.sizes -b 3000 | cut -f1,2,3 > gencode_tss_3kb_flanking.bed