#Overlapping of the bed generated previously using bedtools intersect function
#https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
#Done using  UNIX command line

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#### HUMAN #######
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bedtools intersect -a wgEncodeGencodeComprehensiveV36lift37_fileforhost_filtered.bed \
-b wgEncodeGencodeComprehensiveV36lift37_filefornested_filtered.bed \
-F 1.0 -wo > V36lift37_overlap.bed

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#### MOUSE #######
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bedtools intersect -a wgEncodeGencodeCompVM25_fileforhost_filtered.bed \
-b wgEncodeGencodeCompVM25_filefornested_filtered.bed \
-F 1.0 -wo > VM25_overlap.bed
