Can you please clarify the units for values in Virus_raw_abundance.txt and Virus_normalized_abundance.txt? How is abundance calculated and normalized? The README gives brief definitions for these files:
Virus_raw_abundance.txt # Raw virus genome abundance
Virus_normalized_abundance.txt # Normalized virus genome abundance (normalized by 100M reads/sample)
For each sample, Virus_normalized_abundance.txt includes columns [SampleName] and [SampleName].Percent. There are also MeanCov and MeanCov.Percent values for each vRhyme virus species.
Am I correct to assume that [SampleName] gives mapped reads per 100M reads? And what is the denominator for [SampleName].Percent: the sample-wise column sum (i.e. just reads mapped to identified viruses) or total mapped reads?
Thanks!
Can you please clarify the units for values in
Virus_raw_abundance.txtandVirus_normalized_abundance.txt? How is abundance calculated and normalized? The README gives brief definitions for these files:For each sample,
Virus_normalized_abundance.txtincludes columns[SampleName]and[SampleName].Percent. There are alsoMeanCovandMeanCov.Percentvalues for each vRhyme virus species.Am I correct to assume that
[SampleName]gives mapped reads per 100M reads? And what is the denominator for[SampleName].Percent: the sample-wise column sum (i.e. just reads mapped to identified viruses) or total mapped reads?Thanks!