--- a/makebigwig.sh	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-# 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
-