Given a BED file containing genomic regions of interest (reference) and a set
of other BED files (tabix-indexed), calculate how many samples also
contain the region of interest.
Example:
ref (A)======== (B)============================
sample 1 --- ---- ----- -- ------ ----
sample 2 ---- ------------
sample 3 -----
sample 4 ----
Would return:
sample 1 sample 2 sample 3 sample 4 total
ref A 2 1 0 1 3
ref B 4 1 1 0 3
Usage: bedutils refcount {-ns} ref.bed sample1.bed sample2.bed ...
Where the sample BED files are Tabix indexed (sample1.bed.tgz.tbi exists).
The sample names are calculated using the names of the files.
The reference BED file doesn't need to be Tabix indexed (it is read directly).
Options:
-ns Ignore strandedness in counts
Given a BED file containing genomic regions of interest (reference) and a set
of other BED files (tabix-indexed), calculate how many samples also
contain the region of interest.
Example:
ref (A)======== (B)============================
sample 1 --- ---- ----- -- ------ ----
sample 2 ---- ------------
sample 3 -----
sample 4 ----
Would return:
sample 1 sample 2 sample 3 sample 4 total
ref A 2 1 0 1 3
ref B 4 1 1 0 3
Usage: bedutils refcount {-ns} ref.bed sample1.bed sample2.bed ...
Where the sample BED files are Tabix indexed (sample1.bed.tgz.tbi exists).
The sample names are calculated using the names of the files.
The reference BED file doesn't need to be Tabix indexed (it is read directly).
Options:
-ns Ignore strandedness in counts