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bigWig (update for bedGraphToBigWig ~v357 and later) #29

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bigWig (update for bedGraphToBigWig ~v357 and later) #29

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be385cc
bigWig step:
karl616 Mar 28, 2018
f833045
escaped script internal variables
karl616 Mar 28, 2018
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10 changes: 7 additions & 3 deletions templates/bigwig/RGCRG-ANTISENSE
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,12 @@ samtools view -h -@ ${cpus} ${bam} | \
awk 'BEGIN {OFS="\\t"} {if (\$1!~/^@/) {\$2=xor(\$2,0x10)}; print}' | \
samtools view -@ ${cpus} -Sb - > tmp.bam

genomeCoverageBed -strand + -split -bg -ibam tmp.bam > ${prefix}.plusRaw.bedgraph
genomeCoverageBed -strand - -split -bg -ibam tmp.bam > ${prefix}.minusRaw.bedgraph
genomeCoverageBed -strand + -split -bg -ibam tmp.bam \
| sort -k1,1 -k2,2n \
> ${prefix}.plusRaw.bedgraph
genomeCoverageBed -strand - -split -bg -ibam tmp.bam \
| sort -k1,1 -k2,2n \
> ${prefix}.minusRaw.bedgraph
rm tmp.bam
bedGraphToBigWig ${prefix}.plusRaw.bedgraph ${genomeFai} ${prefix}.plusRaw.bw
bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
10 changes: 7 additions & 3 deletions templates/bigwig/RGCRG-MATE1_SENSE
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,12 @@ samtools view -h -@ ${cpus} ${bam} | \
awk 'BEGIN {OFS="\\t"} {if (\$1!~/^@/ && and(\$2,128)>0) {\$2=xor(\$2,0x10)}; print}' | \
samtools view -@ ${cpus} -Sb - > tmp.bam

genomeCoverageBed -strand + -split -bg -ibam tmp.bam > ${prefix}.plusRaw.bedgraph
genomeCoverageBed -strand - -split -bg -ibam tmp.bam > ${prefix}.minusRaw.bedgraph
genomeCoverageBed -strand + -split -bg -ibam tmp.bam \
| sort -k1,1 -k2,2n \
> ${prefix}.plusRaw.bedgraph
genomeCoverageBed -strand - -split -bg -ibam tmp.bam \
| sort -k1,1 -k2,2n \
> ${prefix}.minusRaw.bedgraph
rm tmp.bam
bedGraphToBigWig ${prefix}.plusRaw.bedgraph ${genomeFai} ${prefix}.plusRaw.bw
bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
10 changes: 7 additions & 3 deletions templates/bigwig/RGCRG-MATE2_SENSE
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,12 @@ samtools view -h -@ ${cpus} ${bam} | \
awk 'BEGIN {OFS="\\t"} {if (\$1!~/^@/ && and(\$2,64)>0) {\$2=xor(\$2,0x10)}; print}' | \
samtools view -@ ${cpus} -Sb - > tmp.bam

genomeCoverageBed -strand + -split -bg -ibam tmp.bam > ${prefix}.plusRaw.bedgraph
genomeCoverageBed -strand - -split -bg -ibam tmp.bam > ${prefix}.minusRaw.bedgraph
genomeCoverageBed -strand + -split -bg -ibam tmp.bam \
| sort -k1,1 -k2,2n \
> ${prefix}.plusRaw.bedgraph
genomeCoverageBed -strand - -split -bg -ibam tmp.bam \
| sort -k1,1 -k2,2n \
> ${prefix}.minusRaw.bedgraph
rm tmp.bam
bedGraphToBigWig ${prefix}.plusRaw.bedgraph ${genomeFai} ${prefix}.plusRaw.bw
bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
6 changes: 4 additions & 2 deletions templates/bigwig/RGCRG-NONE
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
#!/bin/bash -eu
genomeCoverageBed -split -bg -ibam ${bam} > ${prefix}.raw.bedgraph
bedGraphToBigWig ${prefix}.raw.bedgraph ${genomeFai} ${prefix}.raw.bw
genomeCoverageBed -split -bg -ibam ${bam} \
| sort -k1,1 -k2,2n \
> ${prefix}.raw.bedgraph
bedGraphToBigWig ${prefix}.raw.bedgraph ${genomeFai} ${prefix}.raw.bw
10 changes: 7 additions & 3 deletions templates/bigwig/RGCRG-SENSE
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
#!/bin/bash -eu
genomeCoverageBed -strand + -split -bg -ibam ${bam} > ${prefix}.plusRaw.bedgraph
genomeCoverageBed -strand - -split -bg -ibam ${bam} > ${prefix}.minusRaw.bedgraph
genomeCoverageBed -strand + -split -bg -ibam ${bam} \
| sort -k1,1 -k2,2n \
> ${prefix}.plusRaw.bedgraph
genomeCoverageBed -strand - -split -bg -ibam ${bam} \
| sort -k1,1 -k2,2n \
> ${prefix}.minusRaw.bedgraph
bedGraphToBigWig ${prefix}.plusRaw.bedgraph ${genomeFai} ${prefix}.plusRaw.bw
bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
14 changes: 13 additions & 1 deletion templates/bigwig/STAR-ANTISENSE
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,18 @@ if [[ ${wigRefPrefix} != - ]]; then
sed -ni '/^${wigRefPrefix}/p' chrSizes.txt
fi

#make sure the bedGraph files are sorted before converting to bigWig
for bedGraph in Signal/Signal.UniqueMultiple.str1.out.bg \
Signal/Signal.UniqueMultiple.str2.out.bg \
Signal/Signal.Unique.str1.out.bg \
Signal/Signal.Unique.str2.out.bg; do
if [[ ! \$( sort -C -k1,1 -k2,2n \$bedGraph ) ]]; then
sort -k1,1 -k2,2n \$bedGraph > \$bedGraph.sorted && \
mv \$bedGraph.sorted \$bedGraph
fi
done


bedGraphToBigWig Signal/Signal.UniqueMultiple.str1.out.bg \
chrSizes.txt \
${prefix}.UniqueMultiple.minusRaw.bw
Expand All @@ -25,4 +37,4 @@ bedGraphToBigWig Signal/Signal.Unique.str1.out.bg \
${prefix}.Unique.minusRaw.bw
bedGraphToBigWig Signal/Signal.Unique.str2.out.bg \
chrSizes.txt \
${prefix}.Unique.plusRaw.bw
${prefix}.Unique.plusRaw.bw
14 changes: 13 additions & 1 deletion templates/bigwig/STAR-MATE1_SENSE
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,18 @@ if [[ ${wigRefPrefix} != - ]]; then
sed -ni '/^${wigRefPrefix}/p' chrSizes.txt
fi

#make sure the bedGraph files are sorted before converting to bigWig
for bedGraph in Signal/Signal.UniqueMultiple.str1.out.bg \
Signal/Signal.UniqueMultiple.str2.out.bg \
Signal/Signal.Unique.str1.out.bg \
Signal/Signal.Unique.str2.out.bg; do
if [[ ! \$( sort -C -k1,1 -k2,2n \$bedGraph ) ]]; then
sort -k1,1 -k2,2n \$bedGraph > \$bedGraph.sorted && \
mv \$bedGraph.sorted \$bedGraph
fi
done


bedGraphToBigWig Signal/Signal.UniqueMultiple.str1.out.bg \
chrSizes.txt \
${prefix}.UniqueMultiple.plusRaw.bw
Expand All @@ -25,4 +37,4 @@ bedGraphToBigWig Signal/Signal.Unique.str1.out.bg \
${prefix}.Unique.plusRaw.bw
bedGraphToBigWig Signal/Signal.Unique.str2.out.bg \
chrSizes.txt \
${prefix}.Unique.minusRaw.bw
${prefix}.Unique.minusRaw.bw
14 changes: 13 additions & 1 deletion templates/bigwig/STAR-MATE2_SENSE
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,18 @@ if [[ ${wigRefPrefix} != - ]]; then
sed -ni '/^${wigRefPrefix}/p' chrSizes.txt
fi

#make sure the bedGraph files are sorted before converting to bigWig
for bedGraph in Signal/Signal.UniqueMultiple.str1.out.bg \
Signal/Signal.UniqueMultiple.str2.out.bg \
Signal/Signal.Unique.str1.out.bg \
Signal/Signal.Unique.str2.out.bg; do
if [[ ! \$( sort -C -k1,1 -k2,2n \$bedGraph ) ]]; then
sort -k1,1 -k2,2n \$bedGraph > \$bedGraph.sorted && \
mv \$bedGraph.sorted \$bedGraph
fi
done


bedGraphToBigWig Signal/Signal.UniqueMultiple.str1.out.bg \
chrSizes.txt \
${prefix}.UniqueMultiple.minusRaw.bw
Expand All @@ -25,4 +37,4 @@ bedGraphToBigWig Signal/Signal.Unique.str1.out.bg \
${prefix}.Unique.minusRaw.bw
bedGraphToBigWig Signal/Signal.Unique.str2.out.bg \
chrSizes.txt \
${prefix}.Unique.plusRaw.bw
${prefix}.Unique.plusRaw.bw
11 changes: 10 additions & 1 deletion templates/bigwig/STAR-NONE
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,19 @@ if [[ ${wigRefPrefix} != - ]]; then
sed -ni '/^${wigRefPrefix}/p' chrSizes.txt
fi

#make sure the bedGraph files are sorted before converting to bigWig
for bedGraph in Signal/Signal.UniqueMultiple.str1.out.bg \
Signal/Signal.Unique.str1.out.bg; do
if [[ ! \$( sort -C -k1,1 -k2,2n \$bedGraph ) ]]; then
sort -k1,1 -k2,2n \$bedGraph > \$bedGraph.sorted && \
mv \$bedGraph.sorted \$bedGraph
fi
done

bedGraphToBigWig Signal/Signal.UniqueMultiple.str1.out.bg \
chrSizes.txt \
${prefix}.UniqueMultiple.raw.bw

bedGraphToBigWig Signal/Signal.Unique.str1.out.bg \
chrSizes.txt \
${prefix}.Unique.raw.bw
${prefix}.Unique.raw.bw
13 changes: 12 additions & 1 deletion templates/bigwig/STAR-SENSE
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,17 @@ if [[ ${wigRefPrefix} != - ]]; then
sed -ni '/^${wigRefPrefix}/p' chrSizes.txt
fi

#make sure the bedGraph files are sorted before converting to bigWig
for bedGraph in Signal/Signal.UniqueMultiple.str1.out.bg \
Signal/Signal.UniqueMultiple.str2.out.bg \
Signal/Signal.Unique.str1.out.bg \
Signal/Signal.Unique.str2.out.bg; do
if [[ ! \$( sort -C -k1,1 -k2,2n \$bedGraph ) ]]; then
sort -k1,1 -k2,2n \$bedGraph > \$bedGraph.sorted && \
mv \$bedGraph.sorted \$bedGraph
fi
done

bedGraphToBigWig Signal/Signal.UniqueMultiple.str1.out.bg \
chrSizes.txt \
${prefix}.UniqueMultiple.plusRaw.bw
Expand All @@ -25,4 +36,4 @@ bedGraphToBigWig Signal/Signal.Unique.str1.out.bg \
${prefix}.Unique.plusRaw.bw
bedGraphToBigWig Signal/Signal.Unique.str2.out.bg \
chrSizes.txt \
${prefix}.Unique.minusRaw.bw
${prefix}.Unique.minusRaw.bw