downstream analysis

[memphismadison]

Hi 

What is usually used to analyze the output files from RSEG? I have ChIP-Seq samples from matched malignant and normal tissues and ran the data through RSEG. I want to identify the sites that differ between malignant and normal tissue. Malignant person 1, ChIP versus Normal person 1, ChIP. Next, Malignant person 2, ChIP versus Normal person 2, ChIP.

Also, I want to identify what is common between the different malignant tissues. Malignant person 1, ChIP versus Malignant person 2, ChIP versus Malignant person 3, ChIP.

Thanks, Rod

[Song, Qiang]

Hi Rod,

The output file from RSEG follows the  BED file format in UCSC Genome Browser.
We have some in-house programs to do the intersection, union and complement operation to manipulate them.
I think you may also search BEDTools for a set of published tools. Or you may use Galaxy if you are more comfortable with  graphic interface.

What kind of downstream analysis to do really depends on what you want to study. For example, you may examine relationship between
those differentially modified regions and genomic annotations, such as genes, promoters, TFBS, etc. You may also perform motif enrichment
analysis and gene ontology analysis.

I hope these comments will be helpful to you.

Best wishes,
Song Qiang

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