From 1ca0fc367a1097f0a62cdd8a42d962548dd67473 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 25 Jun 2018 14:46:48 -0500
Subject: [PATCH] Add in make tss scripts for mouse.

---
 workflow/scripts/make_tss.sh | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 workflow/scripts/make_tss.sh

diff --git a/workflow/scripts/make_tss.sh b/workflow/scripts/make_tss.sh
new file mode 100644
index 0000000..e1aed9a
--- /dev/null
+++ b/workflow/scripts/make_tss.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+
+cat gencode.gtf |
+grep -P '\tgene\t' |
+grep 'protein_coding' |
+grep -v 'level 3' |
+awk -F '[\t|\"]' '{ print $1"\t"$4"\t"$5"\t"$10"\t0\t"$7 }' |
+awk -F '\t' 'BEGIN{ OFS="\t" } { if ($6=="+") { $3=$2-1; $2=$2-2 } else { $2=$3; $3=$3+1 } print }' |
+sort -k1,1 -k2,2n > gencode.tss
-- 
GitLab