src/hg/makeDb/doc/taeGut1.txt 1.16

Index: src/hg/makeDb/doc/taeGut1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/taeGut1.txt,v
retrieving revision 1.15
retrieving revision 1.16
diff -b -B -U 4 -r1.15 -r1.16
--- src/hg/makeDb/doc/taeGut1.txt	5 Feb 2009 01:17:56 -0000	1.15
+++ src/hg/makeDb/doc/taeGut1.txt	18 Apr 2009 05:13:37 -0000	1.16
@@ -677,4 +677,34 @@
 
 # was earlier...
 # 97507442 bases of 1222864691 (7.974%) in intersection
 
+#############################################################################
+# N-SCAN gene predictions (nscanGene) - (2009-04-17 markd)
+
+/mblab.wustl.edu/predictions/taeGut1
+
+    # obtained NSCAN predictions from michael brent's group
+    # at WUSTL
+    cd /cluster/data/taeGut1/bed/nscan/
+
+    wget -nv http://mblab.wustl.edu/predictions/taeGut1/taeGut1.gtf
+    wget -nv http://mblab.wustl.edu/predictions/taeGut1/taeGut1.prot.fa
+    bzip2 taeGut1.*
+    chmod a-w *
+
+    # load track
+    ldHgGene -bin -gtf -genePredExt taeGut1 nscanGene taeGut1.gtf.bz2
+    hgPepPred taeGut1 generic nscanPep  taeGut1.prot.fa.bz2
+    rm *.tab
+
+    # create zebraFinch/nscanGene.html
+
+    # zebraFinch/taeGut1/trackDb.ra, add:
+    track nscanGene override
+    informant Zerba Finch N-SCAN uses chicken (galGal3) as the informant
+
+    searchTable nscanGene
+    searchType genePred
+    termRegex chr[0-9a-zA-Z_]+\.([0-9]+|pasa)((\.[0-9a-z]+)?\.[0-9a-z]+)?
+    searchPriority 50
+