[Bioc-sig-seq] readAligned and coverage methods of the short read package

[Sirisha Sunkara]

Hello All,

I am looking at read coverage bias in a few samples (some libraries 
constructed under different PCR amplification cycles), and would like to 
look at the coverage plots as % read count distribution/lane  over the  
chromosome/reference coordinates.

Right now reading the export.txt files with the readAligned and the 
coverage methods, I get the raw counts. Is there something that does the 
conversion to % over the total read count/lane before plotting?

Sorry, if I am missing something obvious..

Also, I was wondering if the coverage method retains information of 
regions with "zero" coverage? This would be particularly useful when 
comparing sequencing bias in different samples and/or different library 
construction methods.

Thanks a lot for any pointers,
Sirisha