BEDTools Version 2.7

[quinlana]

Hi all,
I just posted the new version of BEDTools. This was also posted on the BEDTools mailing list, so my apologies to those that were struck twice or thrice.

http://code.google.com/p/bedtools/

Below are the most relevant release notes.
Best,
Aaron


General:

-- "Gzipped" BED and GFF files are now supported as input by all BEDTools. Such files must end in ".gz".
-- Tools that process BAM alignments now uniformly (and properly) compute an ungapped alignment end position based on the BAM CIGAR string. Specifically, "M", "D" and "N" operations are observed when computing the end position.
-- bamToBed requires the BAM file to be sorted/grouped by read id when creating BEDPE output. Note that this is the typical order in which most aligners create SAM/BAM output. This requirement allows the alignment end coordinate for each end of the pair to be properly computed based on its CIGAR string. The same requirement applies to pairToBed.
-- I finally updated the manual.
-- Many unseen modifications to the code that improve clarity and sanity-checking and facilitate future additions/modifications.


New Tool:
-- bedToBam. This utility will converts BED files to BAM format. Both "blocked" (aka BED12) and "unblocked" (e.g. BED6) formats are acceptable. This allows one to, for example, compress large BED files such as dbSNP into BAM format for efficient visualization with IGV, Gambit, and Tablet.


Changes to existing tools:
-- intersectBed
1. Added -wao option to report 0 overlap for features in A that do not intersect any features in B. This is an extension of the -wo option released in v2.6.1.
-- bamToBed
1. Requires that BAM input be sorted/grouped by read name.
-- pairToBed
1. Requires that BAM input be sorted/grouped by read name.
2. Allows use of minimum mapping quality or total edit distance for score field.
-- windowBed
1. Now supports BAM input.
-- genomeCoverageBed
1. -bga option. Allows blocks of zero coverage to be reported in BEDGRAPH format.
2. Eliminated potential seg fault.

[Siva]

RNA-seq ambiguous reads

Hi Aaron
I have done RNA-seq on maize endopserms. I would like to know how does coverageBed handle "ambiguous reads" in RNA-seq experiments? Is there a separate entry that lists such ambiguous reads? I see, in my RNA-seq data, many reads matching mutiple features. Occasionally I also see mRNA reads matching introns. The GFF annotation for maize is not accurate. In addition maize is chock full of retrotransposons that transcribe through various intermediates.

Siva