Merge pull request #51 from ENCODE-DCC/PIP-857_ucsc_croo_tracks

Pip 857 ucsc croo tracks
ENCODE-DCC · Dec 16, 2019 · 2028995 · 2028995
2 parents a67447a + 1de366b
commit 2028995
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Showing 2 changed files with 27 additions and 5 deletions.
diff --git a/.isort.cfg b/.isort.cfg
@@ -3,4 +3,4 @@ multi_line_output=3
 include_trailing_comma=True
 force_grid_wrap=0
 use_parentheses=True
-known_third_party = align,compare_md5,merge_annotation,pandas,pysam,qc_utils,rna_qc,rsem_quant
+known_third_party = compare_md5,merge_annotation,pandas,pysam,qc_utils,rna_qc,rsem_quant
diff --git a/output_definition.json b/output_definition.json
@@ -38,17 +38,39 @@
     }
   },
   "rna.bam_to_signals": {
-    "all": {
+    "all_minus": {
       "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 ${i+1}/signal track of all reads from minus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all minus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off negateValues=on viewLimits=-1:0 transformFunc=LOG maxHeightPixels=64:18:8"
+    },
+    "all_plus": {
+      "path": "bam_to_signals/rep${i+1}/${basename}",
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from plus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all plus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8"
+    },
+    "all_unstranded": {
+      "path": "bam_to_signals/rep${i+1}/${basename}",
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} all\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8"
     },
     "python_log": {
       "path": "bam_to_signals/rep${i+1}/${basename}",
       "table": "Bam_to_signals/Replicate ${i+1}/python log"
     },
-    "unique": {
+    "unique_minus": {
+      "path": "bam_to_signals/rep${i+1}/${basename}",
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from minus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique minus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off negateValues=on viewLimits=-1:0 transformFunc=LOG maxHeightPixels=64:18:8"
+    },
+    "unique_plus": {
+      "path": "bam_to_signals/rep${i+1}/${basename}",
+      "table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from plus strand",
+      "ucsc_track": "track type=bigWig name=\"rep${i+1} unique plus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8"
+    },
+    "unique_unstranded": {
       "path": "bam_to_signals/rep${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 windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8"
     }
   },
   "rna.kallisto": {