Intersectbed Overlap

Question

[Nicolas Rosewick]

Hi,

I've a question about intersectBed. Is it possible to extract only alignment like this :

chromosome ===============================================================
BED/BAM A               ==============              =================
BED FILE B               ============
RESULT                  ==============

But no alignment like this (even if the read overlapp 100% of the feature, I don't want to extract these reads)

chromosome ===============================================================
BED/BAM A    =========================              =================
BED FILE B               =============
RESULT

So, only extracting reads that have 90-95% of its sequence overlapping 90-95% of the feature.

Is it clear ?

Thanks,

N.

Answer 1

[Damian Kao]

There are these options in intersectBed:

-f  Minimum overlap required as a fraction of A.
    - Default is 1E-9 (i.e., 1bp).
    - FLOAT (e.g. 0.50)

-r  Require that the fraction overlap be reciprocal for A and B.
    - In other words, if -f is 0.90 and -r is used, this requires
      that B overlap 90% of A and A _also_ overlaps 90% of B.

[Nicolas Rosewick]

Thanks I didn't see the -t parameter. Sorry

[Nicolas Rosewick]

Thanks I didn't see the -r parameter. Sorry – NicoBxl 0 secs ago

[Nicolas Rosewick]

Thanks I didn't see the -r parameter. Sorry

Answer 2

[Alex Reynolds]

Another option is the use of the bedops tool in the BEDOPS suite, in which you can perform set operations on two (or more) BED files.

For example:

$ bedops -e -90% B.bed A.bed

will return all elements of B.bed which overlap elements in A.bed by 90 or more percent. You can also specify overlap criteria by bases, instead of percent.

There are other set operations and the documentation for bedops provides examples for them, but please let me know if you have any questions.