Hi all,
I updated the BEDTools utility "coverageBed" so that it now reports the density/breadth of coverage for a given interval. Specifically, for each interval in B, it reports:
1) the number of overlapping features in A
2) the number of bases in B that had non-zero coverage from A.
3) the fraction (density) of non-zero bases in B covered by A.
An example (note start coordinates are UCSC 0-based and thus are interpreted to actually be 1 greater):
> cat A.bed
chr1 10 20
chr1 11 21
chr1 12 25
> cat B.bed
chr1 0 50
> coverageBed -a A.bed -b B.bed
chr1 0 50 3 15 50 0.3
where:
column 4 is the number of intervals in A that overlap with B.
column 5 is the number of bases in B with non-zero "coverage" from A.
column 6 is the length of the interval in B.
column 7 is the fraction of bases in B that have non-zero coverage from A.
In essence, this describes the "breadth" of coverage, whereas column 4 describes the "depth". In this case, B is overlapped by 3 features in A and these features cover 30% of the 50bp interval in B.
The newest version is here:
http://people.virginia.edu/~arq5x/bedtools.html OR,
All the best,
Aaron
I updated the BEDTools utility "coverageBed" so that it now reports the density/breadth of coverage for a given interval. Specifically, for each interval in B, it reports:
1) the number of overlapping features in A
2) the number of bases in B that had non-zero coverage from A.
3) the fraction (density) of non-zero bases in B covered by A.
An example (note start coordinates are UCSC 0-based and thus are interpreted to actually be 1 greater):
> cat A.bed
chr1 10 20
chr1 11 21
chr1 12 25
> cat B.bed
chr1 0 50
> coverageBed -a A.bed -b B.bed
chr1 0 50 3 15 50 0.3
where:
column 4 is the number of intervals in A that overlap with B.
column 5 is the number of bases in B with non-zero "coverage" from A.
column 6 is the length of the interval in B.
column 7 is the fraction of bases in B that have non-zero coverage from A.
In essence, this describes the "breadth" of coverage, whereas column 4 describes the "depth". In this case, B is overlapped by 3 features in A and these features cover 30% of the 50bp interval in B.
The newest version is here:
http://people.virginia.edu/~arq5x/bedtools.html OR,
All the best,
Aaron
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