Mercurial > repos > xuebing > bed_to_bigwig
changeset 1:ccd3fd69df1a
Uploaded
| author | xuebing |
|---|---|
| date | Sat, 31 Mar 2012 14:04:04 -0400 |
| parents | abb55c0cfe38 |
| children | c5bf1ec88e4e |
| files | bed_to_bigwig.sh |
| diffstat | 1 files changed, 57 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /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 +