[BioC] I was wondering if anyone here was using SPP?

Thornton, Matthew Matthew.Thornton at med.usc.edu
Mon Mar 18 17:38:41 CET 2013


I have been processing some ChIP-seq data and I looked through the literature and it seemed that spp is indicated as a good program to use.  I have found and adapted the two tutorials I found for using spp, https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq and http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html I have also read the paper.  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? I know that this isn't a bioconductor package, but I think that there are probably quite a few people on this list that are using it and it is hard to find decent information about this program.  Any advice or additional information is greatly appreciated!



Matthew E. Thornton

Research Lab Specialist
Saban Research Institute

USC/Children’s Hospital Los Angeles
513X,  Mail Stop 35
4661 W. Sunset Blvd.
Los Angeles, CA 90027-6020

matthew.thornton at med.usc.edu

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