representation of chipseq and RNA-seq data

Question

[kanwarjag]

I have a two data sets related to same biological experiment (asking same question from different scientific perspective) In RNA-seq I can easily show expression via IGV or similar plots. However in case of Chip seq there is shift in binding from promoter to gene body or vice versa in subset genes from a treatment. Now what I would like to show a single gene both chip seq and RNA seq in one Figure / screen shot. What should be the best strategy. I saw this paper's figure 5 to be closest one what I am thinking. I am sure there may be other better alternatives experts on this forum may have done, Could someone share / point me to the direction the best approach.

[marina.v.yurieva]

I'm not 100% sure and never tried to put ChIP- and RNA-seq together but you might be able to do it in SeqMonk.

Answer 1

[Ying W]

You could do a heatmap kinda thing with gradient for chip-seq showing beginning of gene on one end and end of gene on the other end. If you see shift in binding then the gradient will shift, kinda like the heat map here: http://homer.salk.edu/homer/chipseq/heatmap.html

So maybe a couple heatmaps with before/after that shows the chip-seq shift as well as change in expression

Answer 2

[Irsan]

The easiest way is to view the aligned data (*.bam files) with a genome browser like IGV, IGB (which was used in your provided example) or UCSC genome browser. You can remove the alignment tracks and only keep the coverage tracks, make an SVG screenshot and make it pretty with a vector graphics editor like Inkscape or Adobe Illustrator