From 6208b23aa6add919e728ac518c6046a86e341e90 Mon Sep 17 00:00:00 2001
From: ottojolanki <ojolanki@stanford.edu>
Date: Mon, 16 Dec 2019 13:03:30 -0800
Subject: [PATCH] turn autoscale and smoothing window off

---
 output_definition.json | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/output_definition.json b/output_definition.json
index 48bd10d..0607cdc 100644
--- a/output_definition.json
+++ b/output_definition.json
@@ -40,15 +40,18 @@
   "rna.bam_to_signals": {
     "all_minus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from minus strand"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from minus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all minus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     },
     "all_plus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from plus strand"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from plus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all plus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     },
     "all_unstranded": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     },
     "python_log": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
@@ -56,15 +59,18 @@
     },
     "unique_minus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from minus strand"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from minus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique minus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     },
     "unique_plus": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from plus strand"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from plus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique plus\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     },
     "unique_unstranded": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
-      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads"
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique\" priority=${i+1} visibility=full smoothingWindow=off autoScale=off"
     }
   },
   "rna.kallisto": {