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
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