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Hello all,
I recently posted Version 2.6 of BEDTools. This release includes numerous changes (see below if you want to skip my rambling) and is the first to include ideas and source code directly contributed by other users. Thanks to those who submitted ideas, source code, corrections, etc. I am grateful.
Of widest interest is the native inclusion of BAM support (using BAMTools) to coverageBed and genomeCoverageBed (no longer need to pipe to bamToBed). genomeCoverageBed now also creates BEDGRAPH output and coverageBed will create coverage histograms for _each_ feature in the "B" file. For example, one can compute coverage histograms for each targeted exon, as well as a summary of all targets directly from a BAM file of alignments.
Below is a litany of the specific changes made in this release.
Regards,
Aaron
***Specific improvements / additions to tools***
1. intersectBed
* Added an option (-wo) that reports the number of overlapping bases for each intersection b/w A and B files.
2. coverageBed
* native BAM support
* can now report a histogram (-hist) of coverage for each feature in B. Useful for exome sequencing projects, for example.
* faster
3. genomeCoverageBed
* native BAM support
* can now report coverage in BEDGRAPH format (-bg)
4. bamToBed
* support for "blocked" BED (aka BED12) format (use the -bed12 option). This facilitates the creation of BED entries for "split" alignments (e.g. RNAseq or SV)
-- when using BED12, one can specify an R,G,B color for the output for subsequent uploads to UCSC, Gambit, IGV, Tablet, etc.
5. fastaFromBed
* added the ability to extract sequences from a FASTA file according to the strand in the BED file. That is, when "-" the extracted sequence is reverse complemented.
6. ***NEW*** overlap
* newly added tool for computing the overlap/distance between features on the same line.
I recently posted Version 2.6 of BEDTools. This release includes numerous changes (see below if you want to skip my rambling) and is the first to include ideas and source code directly contributed by other users. Thanks to those who submitted ideas, source code, corrections, etc. I am grateful.
Of widest interest is the native inclusion of BAM support (using BAMTools) to coverageBed and genomeCoverageBed (no longer need to pipe to bamToBed). genomeCoverageBed now also creates BEDGRAPH output and coverageBed will create coverage histograms for _each_ feature in the "B" file. For example, one can compute coverage histograms for each targeted exon, as well as a summary of all targets directly from a BAM file of alignments.
Code:
$ coverageBed -abam reads.bam -b exons.bed -hist
Regards,
Aaron
***Specific improvements / additions to tools***
1. intersectBed
* Added an option (-wo) that reports the number of overlapping bases for each intersection b/w A and B files.
2. coverageBed
* native BAM support
* can now report a histogram (-hist) of coverage for each feature in B. Useful for exome sequencing projects, for example.
* faster
3. genomeCoverageBed
* native BAM support
* can now report coverage in BEDGRAPH format (-bg)
4. bamToBed
* support for "blocked" BED (aka BED12) format (use the -bed12 option). This facilitates the creation of BED entries for "split" alignments (e.g. RNAseq or SV)
-- when using BED12, one can specify an R,G,B color for the output for subsequent uploads to UCSC, Gambit, IGV, Tablet, etc.
5. fastaFromBed
* added the ability to extract sequences from a FASTA file according to the strand in the BED file. That is, when "-" the extracted sequence is reverse complemented.
6. ***NEW*** overlap
* newly added tool for computing the overlap/distance between features on the same line.
Code:
$ cat test.out chr1 10 20 A chr1 15 25 B chr1 10 20 C chr1 25 35 D $ cat test.out | overlaps -i stdin -cols 2,3,6,7 chr1 10 20 A chr1 15 25 B 5 chr1 10 20 C chr1 25 35 D -5
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