src/hg/makeDb/doc/susScr2.txt 1.8

Index: src/hg/makeDb/doc/susScr2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/susScr2.txt,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 4 -r1.7 -r1.8
--- src/hg/makeDb/doc/susScr2.txt	14 Apr 2010 13:35:20 -0000	1.7
+++ src/hg/makeDb/doc/susScr2.txt	19 Apr 2010 04:34:00 -0000	1.8
@@ -792,4 +792,30 @@
 # blastHg18KG 1.627%, ensGene 1.284%, both 0.845%, cover 51.91%, enrich 40.42x
 
     rm -rf blastOut
 #end tblastn
+#############################################################################
+# N-SCAN gene predictions (nscanGene) - (2010-04-18 markd)
+
+/mblab.wustl.edu/predictions/taeGut1
+
+    # obtained NSCAN predictions from michael brent's group
+    # at WUSTL
+    cd /cluster/data/susScr2/bed/nscan
+    wget -nv http://mblab.wustl.edu/predictions/pig/susScr2/readme.txt
+    wget -nv http://mblab.wustl.edu/predictions/pig/susScr2/susScr2.fa
+    wget -nv http://mblab.wustl.edu/predictions/pig/susScr2/susScr2.gtf
+    gzip susScr2.*
+    chmod a-w *
+
+    # load track
+    gtfToGenePred -genePredExt susScr2.gtf.gz stdout | hgLoadGenePred -genePredExt susScr2 nscanGene stdin
+    hgPepPred susScr2 generic nscanPep susScr2.fa.gz
+    rm *.tab
+
+    # pig/susScr2/trackDb.ra, add:
+    track nscanGene override
+    informant Pig N-SCAN uses human (hg19) as the informant, updated with PASA clusters of pig cDNAs.
+
+    # veryify top-level search spec, should produce no results:
+    hgsql -Ne 'select name from nscanGene' susScr2 | egrep -v '^chr[0-9a-zA-Z_]+\.([0-9]+|pasa)((\.[0-9a-z]+)?\.[0-9a-z]+)?$' |head
+############################################################################