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arq5x / bedtools

A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
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Intersect library fragments and not alignment in multibamcov #72

Open dawe opened 11 years ago

dawe commented 11 years ago

I've added an option to multiBamCov which extends one read (R1, right now) for properly paired alignments to the size of ISIZE before the intersection with the bed file. This should, in principle, count intersection of library fragments in place of alignments. I thought this can be useful to have a proper count when dealing with ChIP/MeDIP experiments. A similar option may be considered for genomecov when -bg option is enabled

arq5x commented 11 years ago

Thanks for the contribution! As I understand it, the goal is to count the entire size of the fragment - is that correct?