This question has been discussed number of times in this forum- I have a paculiar situation. I have chips seq data for normal and cancer cells I have used a tool to call peaks and now has bed files which shsiblow enrichment in normal as well as cancer cells. I want to perform K means clustering using TSS as refrence of these peaks. I have used Seqminer to perform clustering I do have results which specifically show that different clusters for normal and cancer cells. The problem is I cannot get a good quality picture. I have tried all differenrt (everything) possible combinations. but picyure come out be very fuzzy. I used 5KB+/- t0 500bp+/- various other adjustments, of no use.
I want to generate fig5 of http://nar.oxfordjournals.org/conten...ar.gkr416.full
or Fig 2E of http://www.ncbi.nlm.nih.gov/pubmed/18992931
Fig1A of http://www.jbc.org/content/early/201...bc.M111.266254
I am also open to use any other tool which can allow me to use bed files for doing K means clustering. I want to stick with my peak calling alogrithm. I undertsand MACS in Galaxy can give such clustering but I have to use MACs peak calling to use such that tool.
Thanks for your help.
I want to generate fig5 of http://nar.oxfordjournals.org/conten...ar.gkr416.full
or Fig 2E of http://www.ncbi.nlm.nih.gov/pubmed/18992931
Fig1A of http://www.jbc.org/content/early/201...bc.M111.266254
I am also open to use any other tool which can allow me to use bed files for doing K means clustering. I want to stick with my peak calling alogrithm. I undertsand MACS in Galaxy can give such clustering but I have to use MACs peak calling to use such that tool.
Thanks for your help.
Comment