diff makebigwig.sh-old @ 20:16ba480adf96

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/makebigwig.sh-old	Sat Mar 31 08:31:22 2012 -0400
@@ -0,0 +1,59 @@
+# make bigwig file for genome browser visulization
+# usage
+# makebigwig.sh <infilename> <outfile> bedorbam sorted genome strand -split
+# input file types: *.bed, *.bam
+
+# 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 "./makebigwig.sh infile outfile bedorbam sorted genome [-split -strand]"
+ exit
+fi
+
+f=$1
+outf=$2
+extension=$3
+sorted=$4
+genome=$5
+strand=$6
+split=$7
+i=i
+echo 'genome:' $genome
+echo 'strand:' $strand
+
+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 -k2,2g $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...=>' $f.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...' $f+.bw
+  bedGraphToBigWig $f+.bedgraph $genome $outf+
+  echo 'making bigwig file for - strand...=>' $f-.bw
+  bedGraphToBigWig $f-.bedgraph $genome $outf-
+ fi
+ rm $f
+