How to zoom out to whole genome view in UCSC browser?

Question

[msimmer92]

Hello, I have custom tracks with my ChIP-seq data on the UCSC browser. I created the bigWig files from the BAM files using deepTools' bamCoverage.

I explored my files in IGV, IGB and UCSC browser. I would like to stick to the third one because has other nice functionalities, but I can´t seem to find the way of zooming out to a genome wide view as I can do with the other two tools. I keep pressing zoom out x100 but it´s still stuck in chromosome 8 showing me the same region, as if it couldn´t go further than that. (the coordinate I am at is: chr8:1-146,364,022 146,364,022 bp). There is a nice trend across the conditions that I would like to visualize genome-wide.

I wondered if this is possible or not. Also, is there a faster way than pressing zoom out x100 all the time until eventually reaching?

(genome: hg19, bamCoverage parameters: -bs 20 --normalizeUsing RPGC --effectiveGenomeSize 2685511504 , I chose that effective genome size because I did MAPQ filtering of reads, so I used the one of the second table that says "use in case you do multimapped reads filtering". Read length 50bp, single-end).

2) Another question: if I did differential binding analysis and normalized using the TMM method (DiffBind package in R), my bigwigs should be also generated with the same normalization, or it´s ok that I chose RPGC? Even though these are not concatenated steps, should I be consistent with the normalization method? or for this particular purpose it´s ok?

Answer 1

[Luis Nassar]

Late to the party here,

As far as your first question, we actually have a lesser known tool that I believe can do what you're asking. The Genome Graph (http://genome.ucsc.edu/cgi-bin/hgGenome) CGI will show you the density of objects located throughout the entire genome. You can import your ChIP-seq onto it and see the distribution.

Here is an example of all the items in the GENCODE v29 track across the genome: http://genome.ucsc.edu/cgi-bin/hgGenome?hgS_doOtherUser=submit&hgS_otherUserName=Lou&hgS_otherUserSessionName=hg38_GenomeGraph

Lou UCSC GB

[msimmer92]

Yes, exactly. That looks great! I did not know this tool. Thank you, I'll give it a try.

Answer 2

[ATpoint]

You cannot zoom out because you reached the boundaries of the chromosome. I do not think the UCSC browser can do what you want, this would be a job for IGV even though I doubt it would be a representative illustration as on that super-large scale some few high-signal events would probably dominate the visualization.

Edit: Maybe a log-transformation (which you can do in IGV) might help reducing the influence of top-enriched regions but (without knowing how your data look), I would probably try to find some representative regions on a single chromosome in order to make a nice figure.

[msimmer92]

Ok, thank you very much! good to know

Answer 3

[msimmer92]

I found another way of doing this, and I leave this here in case someone finds it interesting. With the R package ChIPseeker you can do a "peak coverage plot" across the chromosomes (basically, does the same as the Genome Graph that Luis Nassar mentioned, but still is good to know).

https://www.bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html go to the section called "ChIP peaks coverage plot". It will explain how to do it. There is a command covplot() that does it.

It is not exactly "zooming out" on a browser but the reason I wanted to do that is to obtain something like that, like a global view along the genome, and this also gives you that (I didn't know about this when I asked the question, sorry).