annotate makebigwig.sh @ 13:292186c14b08

Uploaded
author xuebing
date Sat, 10 Mar 2012 08:17:36 -0500
parents b7f1d9f8f3bc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
1 # use of output: move to public_html and visualize in ucsc genome browser with the following:
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
2 # track name="xxx" color=0,0,255 type=bigWig bigDataUrl=http://rous.mit.edu/~wuxbl/xxx.bw
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
3
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
4 if [ $# -lt 6 ]
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
5 then
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
6 echo "./bigwig.sh infile outtag bam/bed sorted/none genome strand/none [-split]"
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
7 exit
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
8 fi
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
9
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
10 f=$1
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
11 outf=$2
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
12 extension=$3
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
13 sorted=$4
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
14 genome=$5
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
15 strand=$6
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
16 split=$7
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
17 i=i
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
18 if [ $extension = bam ]
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
19 then
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
20 i=ibam
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
21 if [ $sorted != sorted ]
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
22 then
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
23 echo 'sorting bam file...=>' $f.sorted.bam
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
24 samtools sort $f $f.sorted
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
25 f=$f.sorted.bam
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
26 fi
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
27 else
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
28 if [ $sorted != sorted ]
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
29 then
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
30 echo 'sorting bed file...=>' $f.sorted.bed
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
31 sort -k1,1 $f > $f.sorted.bed
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
32 f=$f.sorted.bed
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
33 fi
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
34 fi
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
35
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
36 echo 'making bedgraph file...=>' $f.bedgraph
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
37 if [ $strand != strand ]
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
38 then
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
39 genomeCoverageBed -bg -$i $f -g $genome $split > $f.bedgraph
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
40 echo 'making bigwig file...=>' $outf.bw
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
41 bedGraphToBigWig $f.bedgraph $genome $outf
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
42 else
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
43 genomeCoverageBed -bg -$i $f -g $genome $split -strand + > $f+.bedgraph
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
44 genomeCoverageBed -bg -$i $f -g $genome $split -strand - > $f-.bedgraph
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
45 echo 'making bigwig file for + strand...=>' $outf+.bw
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
46 bedGraphToBigWig $f+.bedgraph $genome $outf+.bw
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
47 echo 'making bigwig file for - strand...=>' $outf-.bw
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
48 bedGraphToBigWig $f-.bedgraph $genome $outf-.bw
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
49 fi
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
50
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
51 # remove intermediate files
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
52 if [ $sorted != sorted ]
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
53 then
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
54 rm $f
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
55 fi
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
56 rm $f*.bedgraph
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
57