Sort intervals
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chr order
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Merge intervals
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Intersect intervals
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Report intervals in A that have overlap with at least one interval in B
bedtools intersect -u -a [INPUT_A_BED] -b [INPUT_B_BED]
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Report intervals in A that do not overlap any intervals in B
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Compute jaccard index
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Extract genome sequence for given genomic regions as FASTA file
bedtools getfasta -fi [GENOME_FASTA] -bed [INPUT_BED]
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Only get intervals in A that overlaps with B (at least 1bp)
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Make random intervals of fixed lengths
bedtools random -g [GENOME_FASTA]
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Get x-bp flanking regions for each interval
bedtools flank -i [INPUT_BED] -g [GENOME_SIZE]
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Relative distance metrics
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Output columns
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reldist / count / total / fraction
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If there is no spatial correlation between two interval sets, count and fraction values will show uniform distribution, otherwise show higher fraction in smaller reldist's.
bedtools reldist -a [INPUT_A_BED] -b [INPUT_B_BED]
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Annotate
Only get intervals in A that overlaps with B (at least 50% of A interval)
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Genomic context statistics
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Extend each interval for x-bp towards both direction
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Count overlapping bases
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Get midpoints for all intervals
!cat [INPUT_BED] | awk 'BEGIN {FS=OFS="\t"} {print $1, int(($2+$3)/2), int(($2+$3)/2+1)}' |\
bedtools sort -i stdin > [OUTPUT_BED]
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For each interval in A, assign the closest interval in B (also display the distance)
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For each interval in A.bed, get average signals from B.bedGraph
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For each genomic point in A.bed that has intersection with B.bed, compute relative position in the intersecting interval
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Only take conventional chromosomes
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