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t-neumann / slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity
GNU Affero General Public License v3.0
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How to interpret the bigwig values? #127

Closed gdolsten closed 8 months ago

gdolsten commented 1 year ago

Hi, how do I calculate the values in the .bdg file? I converted the .bdg file, tcreadcount, and the basereadcount .bam files to bws, but I am not able to recreate the bw corresponding to the .bdg from the bw files generated from the tcreadcount and basereadcount. Which one is the best to use for genome pileups?

t-neumann commented 1 year ago

Hi - sorry I need a bit more info. What files exactly did you produce using which command? And what is your overall goal, what do you want to visualize, what is your scientific question?

gdolsten commented 1 year ago

I am trying to visualize the presence/absence of converted (nascent) and non-converted (mature) reads in IGV. To do this, I did two things in parallel: 1. first running alleyoop read-separator, and then running bamCoverage -bs 1 --effectiveGenomeSize on the bam files from read-separator ({filename}_backgroundReads.bam, {filename}_TCReads.bam). 2. I convert the .bedgraph file in /count/ to a .bw using bedGraphToBigWig.

However, these approaches seem to yield different results, and I am not sure which one is better for visualization. For example, if I divide the values from {filename}_TCReads.bw by {filename}_backgroundReads.bw, I do not get the same values as in the /counts/.bedgraph (which goes from 0 to 1)

t-neumann commented 1 year ago

Then you should use the bigwigs you create with bamCoverage on the TCReads and backgroundReads bam files.

The count/bedGraph files give you the conversion rates per T across the genome which are naturally [0,1] but dont give you any indication about converted / unconverted read counts