ChIP-Seq density plot between two groups of genes

Question

[hemantcnaik]

Hello I have Chipseq data(.bam file) from this I have normalized my bam file BPM method and created the density plot using deeptools, density plot i have created for two group of genes (Genes of interest) group of genes are different number in density plot is it effect the interpretation of the data? because gene number are 70 group1 and 30 group2

in this step is it necessary to do peak calling? using only significant peaks i have to do the density plot

And any R related tools alternative to deeptools for density plot? any suggestions

Thank you

[seidel]

What are the questions you are trying to answer? By "density plot" - do you mean a metagene plot where you average the normalized signal profiles across your groups of genes? (or their features, such as TSS?). If so, the differing numbers of genes in each group will not matter to answer the question of whether each group has unique behavior. If you were to then call peaks, what would be the purpose?

As for R related tools, between the GenomicRanges, GenomicFeatures, and rtracklayer libraries, you can crete coverage profiles, normalize the data, and do any sort of comparisons or plots you would like.

Answer 1

[sebastian.gregoricchio]

I do not think it is necessary to perform a peak calling, and the different number of peaks should not be a problem if you perform a statistical test.

As R tools to plot profiles you can use "Rseb" (link). You can start from a deeptools matrix and then perform multiple type of plots, including statistics on the signal. Have a look to the vignette for some examples of what you can do with Rseb.