src/hg/makeDb/doc/h1n1.txt 1.2

Index: src/hg/makeDb/doc/h1n1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/h1n1.txt,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/makeDb/doc/h1n1.txt	27 Apr 2009 03:06:09 -0000	1.1
+++ src/hg/makeDb/doc/h1n1.txt	29 Apr 2009 17:09:49 -0000	1.2
@@ -188,4 +188,25 @@
 
 # load the psl result into humanHA table
     hgLoadPsl h1n1 swineHA.psl
 #################################
+# CREATE h1n1_0429Seq TRACK (DONE.  4/29/09, Fan)
+
+    mkdir –p /hive/data/genomes/h1n1/bed/h1n1_0429Seq
+    cd /hive/data/genomes/h1n1/bed/h1n1_0429Seq
+
+
+# create .fa file
+
+    mkdir -p /gbdb/h1n1/h1n1_0429Seq
+    cp –p ../../download/epiflu_0429_dna_sequence.fasta /gbdb/h1n1/h1n1_0429Seq
+
+    hgLoadSeq –replace h1n1 /gbdb/h1n1/h1n1_0429Seq/epiflu_0429_dna_sequence.fasta 
+
+
+# BLAT
+    gfClient -minScore=200 -minIdentity=80 -nohead hgwdev.cse.ucsc.edu 18892  /gbdb/h1n1/nib \
+    -out=psl -t=dna -q=dna /gbdb/h1n1/h1n1_0429Seq/epiflu_0429_dna_sequence.fasta h1n1_0429Seq.psl
+
+# load the psl result into h1n1_0429Seq table
+    hgLoadPsl h1n1 h1n1_0429Seq.psl
+