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languagebash
titleclick here for the bedtools subtract code and output

My output is commented in this code block.

Code Block
languagebash
cd subtract 
module load bedtools #if you haven't loaded it up yet this session
bedtools subtract -a gencode.v19.genes.sort.merge.final -b gencode.v19.proteincoding.genes.sort.merge.final > gencode.v19.notproteincodingnot.proteincoding.genes.bed

wc -l gencode.v19.not.proteincoding.genes.bed
#23483 gencode.v19.not.notproteincodingproteincoding.genes.bed

more gencode.v19.not.proteincoding.genes.bed
#chr1    11869    14412    DDX11L1    .    +
#chr1    14363    29806    WASH7P    .    -
#chr1    29554    31109    MIR1302-11    .    +
#chr1    34554    36081    FAM138A    .    -
#chr1    52473    54936    OR4G4P    .    +
#chr1    62948    63887    OR4G11P    .    +

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