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Hi all,
I am releasing a new version of BEDTools that addresses many of the requests that I've received over the last month. It took me a bit to find time to incorporate the changes. I hope the new functionality proves useful to those that use the BEDTools suite.
The source is posted here: http://people.virginia.edu/~arq5x/bedtools.html
as well as on SourceForge.
All the best,
Aaron
=== Notable changes in this release ===
1. coverageBed will (optionally) only count features in BED file A (e.g. sequencing reads) that overlap with the intervals/windows in BED file B on the same strand. This has been requested several times recently and facilitates CHiP-Seq and RNA-Seq experiments.
2. intersectBed can now require a minimum __reciprocal__ overlap between intervals in BED A and BED B. For example, previously, if one used -f 0.90, it required that a feature in B overlap 90% of the feature in A for the "hit" to be reported. If one adds the -r (reciprocal) option, the hit must also cover 90% of the feature in B. This helps to exclude overlaps between say small features in A and large features in B:
A ==========
B *********************************************
-f 0.50 (Reported), whereas -f 0.50 -r (Not reported)
3. The score field has been changed to be a string. While this deviates from the UCSC definition, it allows one to track much more meaningful information about a feature/interval. For example, score could now be:
7.31E-05 (a p-value)
0.334577 (mean enrichment)
2:2.2:40:2 (several values encoded in a string)
4. closestBed now, by default, reports __all__ intervals in B that overlap equally with an interval in A. Previously, it merely reported the first such feature that appeared in B. Using the -t option, one can also choose to report either the first or the last entry in B in the event of a tie.
5. Several other minor changes to the algorithms have been made to increase speed a bit.
I am releasing a new version of BEDTools that addresses many of the requests that I've received over the last month. It took me a bit to find time to incorporate the changes. I hope the new functionality proves useful to those that use the BEDTools suite.
The source is posted here: http://people.virginia.edu/~arq5x/bedtools.html
as well as on SourceForge.
All the best,
Aaron
=== Notable changes in this release ===
1. coverageBed will (optionally) only count features in BED file A (e.g. sequencing reads) that overlap with the intervals/windows in BED file B on the same strand. This has been requested several times recently and facilitates CHiP-Seq and RNA-Seq experiments.
2. intersectBed can now require a minimum __reciprocal__ overlap between intervals in BED A and BED B. For example, previously, if one used -f 0.90, it required that a feature in B overlap 90% of the feature in A for the "hit" to be reported. If one adds the -r (reciprocal) option, the hit must also cover 90% of the feature in B. This helps to exclude overlaps between say small features in A and large features in B:
A ==========
B *********************************************
-f 0.50 (Reported), whereas -f 0.50 -r (Not reported)
3. The score field has been changed to be a string. While this deviates from the UCSC definition, it allows one to track much more meaningful information about a feature/interval. For example, score could now be:
7.31E-05 (a p-value)
0.334577 (mean enrichment)
2:2.2:40:2 (several values encoded in a string)
4. closestBed now, by default, reports __all__ intervals in B that overlap equally with an interval in A. Previously, it merely reported the first such feature that appeared in B. Using the -t option, one can also choose to report either the first or the last entry in B in the event of a tie.
5. Several other minor changes to the algorithms have been made to increase speed a bit.