--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_to_bigwig.sh	Sat Mar 31 14:04:04 2012 -0400
@@ -0,0 +1,57 @@
+# use of output: move to public_html and visualize in ucsc genome browser with the following:
+# track name="xxx" color=0,0,255 type=bigWig bigDataUrl=http://rous.mit.edu/~wuxbl/xxx.bw
+
+if [ $# -lt 6 ]
+then
+ echo "./bigwig.sh infile outtag bam/bed sorted/none genome strand/none [-split]"
+ exit
+fi
+
+f=$1
+outf=$2
+extension=$3
+sorted=$4
+genome=$5
+strand=$6
+split=$7
+i=i
+if [ $extension = bam ]
+then
+ i=ibam
+ if [ $sorted != sorted ]
+ then
+   echo 'sorting bam file...=>' $f.sorted.bam
+   samtools sort $f $f.sorted
+   f=$f.sorted.bam
+ fi
+else
+ if [ $sorted != sorted ]
+ then
+   echo 'sorting bed file...=>' $f.sorted.bed
+   sort -k1,1 $f > $f.sorted.bed
+   f=$f.sorted.bed
+ fi
+fi
+
+ echo 'making bedgraph file...=>' $f.bedgraph
+ if [ $strand != strand ]
+ then
+  genomeCoverageBed -bg -$i $f -g $genome $split > $f.bedgraph
+  echo 'making bigwig file...=>' $outf.bw
+  bedGraphToBigWig $f.bedgraph $genome $outf
+ else
+  genomeCoverageBed -bg -$i $f -g $genome $split -strand + > $f+.bedgraph
+  genomeCoverageBed -bg -$i $f -g $genome $split -strand - > $f-.bedgraph
+  echo 'making bigwig file for + strand...=>' $outf+.bw
+  bedGraphToBigWig $f+.bedgraph $genome $outf+.bw
+  echo 'making bigwig file for - strand...=>' $outf-.bw
+  bedGraphToBigWig $f-.bedgraph $genome $outf-.bw
+ fi
+
+# remove intermediate files
+if [ $sorted != sorted ]
+  then
+   rm $f
+fi
+rm $f*.bedgraph
+