title: ChIP-seq data processing and the output of the program SPP
body: <p>I have been processing some ChIP-seq data with spp. I looked through the literature and it seemed that spp is indicated as a good program to use (ENCODE uses it). I have found and adapted the two tutorials I found for using spp, <a href="https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq" rel="nofollow">https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq</a> and <a href="http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html" rel="nofollow">http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html</a> I have also read the paper...ncbi.nlm.nih.gov/pubmed/19029915. I have also e-mailed Prof. Karchencko and posted on the bioconductor listserv - all with no response. My question is about the MSER and the predicted sequencing depth - additional output of spp. So what I think the MSER is, is the score value above which a peak is authoritatively determined? When I look at peaks above this score value they are very well defined. Also, is the predicted sequencing depth is a prediction of the number of additional "tags" necessary so that the MSER and the FDR value coincide? It is hard to find decent information about this program. Any advice or additional information is greatly appreciated!</p>
  
  <p>TIA</p>