Question: multibamsummary vs multibigwigsummary
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gravatar for skhil083
5 weeks ago by
skhil0830
skhil0830 wrote:

I am in the process of comparing the similarity between two ChIP-seq conditions. According to the Deeptools documents, multibamsummary computes the read coverages for genomic regions for typically two or more BAM files whereas multibigwigsummary computes the average scores for each of the files in every genomic region.

I am having difficulty understanding the difference between the two tools and which one I should use. What is the difference between read coverage and average scores? Does the scale of the average score change depending on sequencing depth? Could someone shed some light on this please? Thank you in advance.

galaxy chip-seq • 88 views
ADD COMMENTlink modified 5 weeks ago by Devon Ryan1.8k • written 5 weeks ago by skhil0830
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gravatar for Devon Ryan
5 weeks ago by
Devon Ryan1.8k
Germany
Devon Ryan1.8k wrote:

The scale of read coverage will vary with sequencing depth, so multiBamSummary is always affected by this. This is the benefit of making bigWig files and then using multiBigwigSummary, since you can use either bamCoverage or bamCompare (or bigwigCompare after bamCoverage) to first normalize sequencing depth or to input samples in some reasonable way before summarizing by region or bin. Consequently, I suggest that people use multiBigwigSummary instead of multiBamSummary.

ADD COMMENTlink written 5 weeks ago by Devon Ryan1.8k

My bigwig files were created with bedgraphtoBigwig following stretching with slopBed. Would that still be appropriate to use for multibigwigsummary? Since the scale of multibigwigsummary corresponds to average read scores calculated, would higher scores theoretically correspond to peaks with greater height or would it be width?

ADD REPLYlink written 5 weeks ago by skhil0830

You can make the bigWig files from whatever you like. It's impossible to tell whether higher signal in a given bin corresponds to greater signal width vs. greater height. It's simply showing a greater average signal.

ADD REPLYlink written 5 weeks ago by Devon Ryan1.8k

So what is the biological translation of that greater average signal, if we are to assume the experiment was done well. Would it be greater transcription factor binding per se?

ADD REPLYlink written 4 weeks ago by skhil0830

Yes, it's more of whatever you're IPing in that area.

ADD REPLYlink written 4 weeks ago by Devon Ryan1.8k
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