Hi,
I was wondering of there was any package implementing a peak calling method that would take paired-end data (for ATACseq precisely).
I am checked the packages narrowPeaks, BayesPeaks and SPP (which is not in bioconductor), but none seems to work with paired-end data.
I am currently using macs2, which works fine, but as I do all further step in R, it would have come handy to have an R software do to this step as well.
csaw works with paired-end reads. It won't call peaks for an individual library in isolation, but it can compare a ChIP library to input.
Hi,
I am not aware of any ChIP-seq peak-callers that specifically use the paired-end information, rather than just pretending the reads are single-end. Historically, paired-end ChIP-seq is pretty rare compared to single-end, which is probably why the problem has not been addressed fully. Of course, ATAC-seq has big differences from ChIP-seq. Perhaps a paired-end peak-caller will be of much greater value in this setting; somebody more familiar with ATAC-seq may be able to offer you an opinion.
As far as ChIP-seq analysis goes, two big advantages of paired-end data are 1) more specific removal of PCR duplicates and 2) better estimation of average fragment length, both of which can often be done as pre-processing steps without a paired-end specific peak-caller. Then, the data can be fed in to your favourite peak-caller as single-end reads. How appropriate that is for ATAC-seq analysis is something I don't feel qualified to say with any certainty.
from https://groups.google.com/forum/#!searchin/macs-announcement/BAMPE/macs-announcement/Vh916L3tOOE/TUjLeQtsCfkJ :
"In BAMPE mode, the 5’ end plus the observed template length will both be recorded so in later analysis, MACS2 piles up the actual entire observed fragment/template instead of estimating a fixed DNA fragment length"
So it looks like they do not comptue an average length, but use the indicated fragment length for each fragment :)
Hi,
I think for ATAC-seq you might consider peak callers that have worked good with DNase. Have a look to this paper
Koohy H, Down TA, Spivakov M, Hubbard T (2014) A Comparison of Peak Callers Used for DNase-Seq Data. PLoS ONE 9(5): e96303.
We also reviewed many peak callers here (ChIP-seq only)
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326.
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version 2.3.6
Thanks Gordon! In the case of ATAC we do not have a background/input to compare to (like DNAse), but I could use the method of filtering by local enrichment you propose in the csaw user guide, to mimic peak calling. Thanks!