RNA-seq data can have specific biases at either the 5’ or 3’ end of sequenced fragments.

plot5Prime3PrimeBias(object, ...)

Value

ggplot.

Details

It is common to see a small amount of bias, especially if polyA enrichment was performed, or if there is any sample degradation. If a large amount of bias is observed here, be sure to analyze the samples with a Bioanalyzer and check the RIN scores.

5' (3') bias is generally calculated as the median of the following ratio:

[mean expression of 5' (3')] /
[mean expression of whole transcript]


For example:

• Mean expression for 5' (3') is calculated as mean coverage of first (last) 100 bases.

• Mean expression of transcript is the mean coverage of all bases in that transcript.

• Median is calculated for the representative set of 1000 transcripts.

Examples

class(plot5Prime3PrimeBias)#> [1] "nonstandardGenericFunction"
#> attr(,"package")
#> [1] "methods"