From 9603f55e00d56ac267f88030d189bf430d6cea15 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Wed, 18 Jan 2017 11:17:16 -0600
Subject: [PATCH] Update code for protein coding genes tss.

---
 excluded_regions_processing.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/excluded_regions_processing.sh b/excluded_regions_processing.sh
index 5fc3582..2f699dc 100644
--- a/excluded_regions_processing.sh
+++ b/excluded_regions_processing.sh
@@ -1,4 +1,7 @@
 # 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
-- 
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