src/hg/makeDb/doc/susScr2.txt 1.8
1.8 2010/04/19 04:34:00 markd
add N-SCAN to susScr2
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
+############################################################################