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afrendeiro/annotateTSSs.sh

Created January 27, 2014 23:13
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Takes a bed file with gene annotation ("annotationFile.bed") and makes another with TSS annotation ("annotationFile.TSSs.bed")
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annotateTSSs.sh
awk -v OFS='\t' '$6 == "+" {print $1, $2, $2+1, $4, $5, $6}' annotationFile.bed > tmp
awk -v OFS='\t' '$6 == "-" {print $1, $3, $3+1, $4, $5, $6}' annotationFile.bed >> tmp
bedtools sort -i tmp > annotationFile.TSSs.bed
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