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Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes
Figure 5
Estimation of required sequencing coverage for detection of a homologous region.
Probability of successful region construction by Virana depending on the lengths of the transcripts being sought, the region linkage parameter 
, as well as characteristics of the sequencing platform employed. Colored areas represent overlapping standard error bands of the mean, denoting the uncertainties of the estimations. The probability of Virana to detect a homologous region depends on the length of the viral transcript being sought, the linkage parameter 
of the homologous region, as well as the transcript coverage and read length of the sequencing platform employed. Given characteristics of the sequencing process applied for NB1 sample panel, an average viral cDNA of length 
bp requires a minimal transcript coverage of 
in order to be reliably detected using a linkage parameter of 
as employed in this study (upper left quadrant, dashed blue vertical line). Technologies affording longer read length as used for the NB2 panel typically also afford higher sequencing depths. However, at a fixed coverage these technologies generate a more highly fragmented region linkage due to a smaller number of longer reads, resulting in lower probability of generating contiguous homologous regions (lower left quadrant). Lower transcript coverage is sufficient for longer transcripts transcribed from a complete A-MuLV genome (upper right panel, dotted black vertical line) or smaller values of the region linkage parameter 
.
doi: https://doi.org/10.1371/journal.pcbi.1003228.g005