SEQanswers

Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bioanalyzer/TapeStation fragment sizes larger than agarose gel cpylant Sample Prep / Library Generation 2 10-30-2017 06:48 AM
Amplicon resolving differently between bioanalyzer and tapestation Pab77 Sample Prep / Library Generation 3 01-25-2016 02:41 PM
Inconsistensies in RINs between Bioanalyzer and Tapestation Holioneok Sample Prep / Library Generation 8 12-02-2015 06:11 PM
Agilent Bioanalyzer alternatives? rmetz Sample Prep / Library Generation 20 06-18-2015 12:14 AM
RNA Integrity on Agilent's Bioanalyzer jvelotta RNA Sequencing 0 05-07-2013 01:15 PM

Reply
 
Thread Tools
Old 03-31-2020, 03:36 AM   #1
jwfoley
Senior Member
 
Location: Stanford

Join Date: Jun 2009
Posts: 181
Default 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.
jwfoley is offline   Reply With Quote
Old 03-31-2020, 06:50 PM   #2
luc
Senior Member
 
Location: US

Join Date: Dec 2010
Posts: 436
Default

Thanks!!!
This is a neat idea.
luc is offline   Reply With Quote
Old 04-01-2020, 04:26 AM   #3
Marc_Jones
Member
 
Location: UK

Join Date: Jun 2017
Posts: 10
Default

Made it to CRAN yet?
Marc_Jones is offline   Reply With Quote
Old 04-01-2020, 09:24 AM   #4
jwfoley
Senior Member
 
Location: Stanford

Join Date: Jun 2009
Posts: 181
Default

Quote:
Originally Posted by Marc_Jones View Post
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.
jwfoley is offline   Reply With Quote
Reply

Tags
bioanalyzer, electrophoresis, tapestation

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:25 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO