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Loop bedtools command over multiple files

I need to loop through bedtools over multiple files. There are 40 files that i should perform bedtools intersect with another file on shell. This is what i gave:

for i in temp*
do
bedtools intersect -a A.bed -b $i -v
done

However, this did not work. Is there anyother way that this can be done?

software error
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updated by Alex Reynolds Alex Reynolds • written by aishwaryamandava7 • aishwaryamandava7

Try putting the -v before the -a.

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written by novice novice

1 answer

Without using a loop:

$ bedops --not-element-of 1 A.bed temp*.bed > answer.bed
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written by Alex Reynolds Alex Reynolds

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