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