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-a and -b indicate what files to intersect. in -b, you can specify one, or several files to intersect with the file specified in -a.
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| title | bedtools intersect options |
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- wa: Write the original entry in A for each overlap.
- wb: Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by -f and -r.
- loj: Perform a “left outer join”. That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B.
- wo: Write the original A and B entries plus the number of base pairs of overlap between the two features. Only A features with overlap are reported. Restricted by -f and -r.
- wao: Write the original A and B entries plus the number of base pairs of overlap between the two features. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. Restricted by -f and -r.
- f: Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
- v: Only report those entries in A that have no overlap in B. Restricted by -f and -r. Useful to report what doesn't overlap, the inverse of typical usage.
- names: When using multiple databases (-b), provide an alias for each that will appear instead of a file Id when also printing the DB record.
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