Mercurial > repos > xuebing > sharplab_interval_analysis

comparison makebigwig.sh-old @ 20:16ba480adf96

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author xuebing
date Sat, 31 Mar 2012 08:31:22 -0400
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19:d325683ec368 20:16ba480adf96
1 # make bigwig file for genome browser visulization
2 # usage
3 # makebigwig.sh <infilename> <outfile> bedorbam sorted genome strand -split
4 # input file types: *.bed, *.bam
5
6 # use of output: move to public_html and visualize in ucsc genome browser with the following:
7 # track name="xxx" color=0,0,255 type=bigWig bigDataUrl=http://rous.mit.edu/~wuxbl/xxx.bw
8
9 if [ $# -lt 6 ]
10 then
11 echo "./makebigwig.sh infile outfile bedorbam sorted genome [-split -strand]"
12 exit
13 fi
14
15 f=$1
16 outf=$2
17 extension=$3
18 sorted=$4
19 genome=$5
20 strand=$6
21 split=$7
22 i=i
23 echo 'genome:' $genome
24 echo 'strand:' $strand
25
26 if [ $extension = bam ]
27 then
28 i=ibam
29 if [ $sorted != sorted ]
30 then
31 echo 'sorting bam file...=>' $f.sorted.bam
32 samtools sort $f $f.sorted
33 f=$f.sorted.bam
34 fi
35 else
36 if [ $sorted != sorted ]
37 then
38 echo 'sorting bed file...=>' $f.sorted.bed
39 sort -k1,1 -k2,2g $f > $f.sorted.bed
40 f=$f.sorted.bed
41 fi
42 fi
43
44 echo 'making bedgraph file...=>' $f.bedgraph
45 if [ $strand != strand ]
46 then
47 genomeCoverageBed -bg -$i $f -g $genome $split > $f.bedgraph
48 echo 'making bigwig file...=>' $f.bw
49 bedGraphToBigWig $f.bedgraph $genome $outf
50 else
51 genomeCoverageBed -bg -$i $f -g $genome $split -strand + > $f+.bedgraph
52 genomeCoverageBed -bg -$i $f -g $genome $split -strand - > $f-.bedgraph
53 echo 'making bigwig file for + strand...' $f+.bw
54 bedGraphToBigWig $f+.bedgraph $genome $outf+
55 echo 'making bigwig file for - strand...=>' $f-.bw
56 bedGraphToBigWig $f-.bedgraph $genome $outf-
57 fi
58 rm $f
59