Hi all,
I'm looking for a tool which will allow me to plot the strand cross correlation of reads in some ChIp-seq data.
The estimate.mean.fraglen() function in the chipseq R package uses a correlation method to estimate fragment size, but gives me an answer far off what I'd expect - ~570bp rather than 200bp. The other methods the function can use give me ~200bp (SISSR) and ~380bp (coverage).
I'd like to plot the strand cross correlation to see why this might be happening. I've found this tool: http://code.google.com/p/phantompeakqualtools/, which is based on SPP (http://compbio.med.harvard.edu/Supplements/ChIP-seq/) but I am having trouble installing all the necessary dependencies on the lab server. Does anyone know of any alternatives? I don't need the peak-calling functionality of SPP, just the correlation plots.
Thank you!
I'm looking for a tool which will allow me to plot the strand cross correlation of reads in some ChIp-seq data.
The estimate.mean.fraglen() function in the chipseq R package uses a correlation method to estimate fragment size, but gives me an answer far off what I'd expect - ~570bp rather than 200bp. The other methods the function can use give me ~200bp (SISSR) and ~380bp (coverage).
I'd like to plot the strand cross correlation to see why this might be happening. I've found this tool: http://code.google.com/p/phantompeakqualtools/, which is based on SPP (http://compbio.med.harvard.edu/Supplements/ChIP-seq/) but I am having trouble installing all the necessary dependencies on the lab server. Does anyone know of any alternatives? I don't need the peak-calling functionality of SPP, just the correlation plots.
Thank you!
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