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#after the creation of the first file
cat yeast_pairedend_sort.mapped.q1.merge.bed | awk '{print $1 "\t" $2 "\t" $3 "\t" $5 "\t" $6 "\t" $4}' > yeast_pairedend_sort.mapped.q1.merge.bed

#piped in-line
bedtools merge -s -c 4,5 -o count_distinct,sum -i yeast_pairedend_sort.mapped.q1.bed | awk '{print $1 "\t" $2 "\t" $3 "\t" $5 "\t" $6 "\t" $4}' > yeast_pairedend_sort.mapped.q1.merge.bed

 bedtools intersect: identifying where two experiments overlap (or don't overlap)

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Using the options we've specified (-wo) the resulting file will have entries for file A, file B and the number of base pairs overlap between the feature in A and the features in B, but we'll only retain lines where there is an overlap between A and B.  We could also use the -v option to only contain areas with NO intersection, or control the intersections with -f and -r options.  Bedtools intersect is a powerful tool, and it's always a good idea to ask "what is this code going to do?" while you're testing analysis workflows.  It can be very useful to pipe your output to more when you are unsure of the output of a command, as such:

bedtools intersect -wo -a human_rnaseq_bwa_sort.mapped.q1.merge.bed -b human_mirnaseq_hg19_sort.mapped.q1.merge.bed | more

bedtools closest: when you want to know how far your regions are from a test set

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