Mercurial > repos > xuebing > bed_to_bigwig

comparison bed_to_bigwig.sh @ 1:ccd3fd69df1a

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author xuebing
date Sat, 31 Mar 2012 14:04:04 -0400
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0:abb55c0cfe38 1:ccd3fd69df1a
1 # use of output: move to public_html and visualize in ucsc genome browser with the following:
2 # track name="xxx" color=0,0,255 type=bigWig bigDataUrl=http://rous.mit.edu/~wuxbl/xxx.bw
3
4 if [ $# -lt 6 ]
5 then
6 echo "./bigwig.sh infile outtag bam/bed sorted/none genome strand/none [-split]"
7 exit
8 fi
9
10 f=$1
11 outf=$2
12 extension=$3
13 sorted=$4
14 genome=$5
15 strand=$6
16 split=$7
17 i=i
18 if [ $extension = bam ]
19 then
20 i=ibam
21 if [ $sorted != sorted ]
22 then
23 echo 'sorting bam file...=>' $f.sorted.bam
24 samtools sort $f $f.sorted
25 f=$f.sorted.bam
26 fi
27 else
28 if [ $sorted != sorted ]
29 then
30 echo 'sorting bed file...=>' $f.sorted.bed
31 sort -k1,1 $f > $f.sorted.bed
32 f=$f.sorted.bed
33 fi
34 fi
35
36 echo 'making bedgraph file...=>' $f.bedgraph
37 if [ $strand != strand ]
38 then
39 genomeCoverageBed -bg -$i $f -g $genome $split > $f.bedgraph
40 echo 'making bigwig file...=>' $outf.bw
41 bedGraphToBigWig $f.bedgraph $genome $outf
42 else
43 genomeCoverageBed -bg -$i $f -g $genome $split -strand + > $f+.bedgraph
44 genomeCoverageBed -bg -$i $f -g $genome $split -strand - > $f-.bedgraph
45 echo 'making bigwig file for + strand...=>' $outf+.bw
46 bedGraphToBigWig $f+.bedgraph $genome $outf+.bw
47 echo 'making bigwig file for - strand...=>' $outf-.bw
48 bedGraphToBigWig $f-.bedgraph $genome $outf-.bw
49 fi
50
51 # remove intermediate files
52 if [ $sorted != sorted ]
53 then
54 rm $f
55 fi
56 rm $f*.bedgraph
57