Question: How to zoom out to whole genome view in UCSC browser?
gravatar for msimmer92
16 months ago by
msimmer92250 wrote:

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?

browser bigwig ucsc • 559 views
ADD COMMENTlink modified 15 months ago • written 16 months ago by msimmer92250
gravatar for Luis Nassar
16 months ago by
Luis Nassar390
UCSC Genome Browser
Luis Nassar390 wrote:

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 ( 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:


ADD COMMENTlink written 16 months ago by Luis Nassar390

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

ADD REPLYlink written 15 months ago by msimmer92250
gravatar for ATpoint
16 months ago by
ATpoint36k wrote:

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.

ADD COMMENTlink modified 16 months ago • written 16 months ago by ATpoint36k

Ok, thank you very much! good to know

ADD REPLYlink written 16 months ago by msimmer92250
gravatar for msimmer92
15 months ago by
msimmer92250 wrote:

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). 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).

ADD COMMENTlink modified 15 months ago • written 15 months ago by msimmer92250
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