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Bedtools BEDMAP usage

Can bedtools bedmap be used in a for loop? Can we overwrite the output file using >> ?

assembly genome next-gen
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written by bioinfo456 bioinfo456

Standard rules of shell usage apply, nothing special with these tools. If you give a representative example and show what you've tried we can try to debug.

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written by ATpoint ATpoint 
 foreach ($v1 as $value) {
$outputh = system("/home/uday/anaconda3/bin/bedmap --chrom ". $value ." --mean ppCkrtYdyJ_3.bed pc.bed >> ppCkrtYdyJ_f10.txt");
}

v1 contains unique chromosomes. I'm getting an empty file as output.

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written by bioinfo456 bioinfo456

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