bioanalyzeR: New R package for data from the Agilent Bioanalyzer and TapeStation

jwfoley · 03-31-2020, 04:36 AM

I wrote an R package for importing electrophoresis data from the Agilent Bioanalyzer and TapeStation and graphing the results with ggplot2 or analyzing them in more depth:

package on GitHub
vignette

One particular application is for sequencing library QC, where the variable of interest is the size distribution of your sample by molarity, but the Agilent software only shows you total fluorescence, which is proportional to mass instead of molarity and therefore gives you a misleading representation.

For example, here's the same library shown with fluorescence vs. log-scaled molecule length (analogous to the Agilent software's display) and then with molarity/bp vs. linear-scaled length (so area under the curve is molarity):

And the package includes a function to automatically calculate the molar ratio of good inserts to bad adapter dimers in Illumina sequencing libraries.

This is a work in progress so I would be grateful for any feedback.

luc · 03-31-2020, 07:50 PM

Thanks!!!
This is a neat idea.

Marc_Jones · 04-01-2020, 05:26 AM

Made it to CRAN yet?

jwfoley · 04-01-2020, 10:24 AM

Quote:

Originally Posted by Marc_Jones

Made it to CRAN yet?

Considering that or Bioconductor. It doesn't have any Bioconductor dependencies so CRAN might be easier for everyone involved, but on the other hand some of the homebrew data structures might be better implemented with Bioconductor tools and I haven't looked into that yet.

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03-31-2020, 04:36 AM	#1
jwfoley Senior Member Location: Stanford Join Date: Jun 2009 Posts: 181	bioanalyzeR: New R package for data from the Agilent Bioanalyzer and TapeStation I wrote an R package for importing electrophoresis data from the Agilent Bioanalyzer and TapeStation and graphing the results with ggplot2 or analyzing them in more depth: package on GitHub vignette One particular application is for sequencing library QC, where the variable of interest is the size distribution of your sample by molarity, but the Agilent software only shows you total fluorescence, which is proportional to mass instead of molarity and therefore gives you a misleading representation. For example, here's the same library shown with fluorescence vs. log-scaled molecule length (analogous to the Agilent software's display) and then with molarity/bp vs. linear-scaled length (so area under the curve is molarity): And the package includes a function to automatically calculate the molar ratio of good inserts to bad adapter dimers in Illumina sequencing libraries. This is a work in progress so I would be grateful for any feedback.

03-31-2020, 07:50 PM	#2
luc Senior Member Location: US Join Date: Dec 2010 Posts: 452	Thanks!!! This is a neat idea.

04-01-2020, 05:26 AM	#3
Marc_Jones Member Location: UK Join Date: Jun 2017 Posts: 10	Made it to CRAN yet?