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