rnaf: Model of positional bias that can arise when RNA-seq is...

In alyssafrazee/polyester: Simulate RNA-seq reads

Description

This positional bias model was estimated in Li and Jiang (2012). With RNA fragmentation, reads are more likely to have come from the middle of the transcript than either end. The probabilities included in this dataset were estimated from Supplementary Figure S3 in Li and Jiang's manuscript. Data points from the figure were inferred and exported as CSV files using WebPlotDigitizer. The CSV files and the code used to process them and create the datasets are available in the Polyester GitHub repository (https://github.com/alyssafrazee/polyester).

Format

data frame with 100 rows and 2 columns. Column 1 is position along a transcript (in percent), while Column 2 is the probability of getting a fragment at that position. Column 2 sums to 1.

References

Li W and Jiang T (2012): Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads. Bioinformatics 28(22): 2914-2921.

Rohatgi A (2014): WebPlotDigitizer: Version 3.4 of WebPlotDigitizer. ZENODO. 10.5281/zenodo.11835

alyssafrazee/polyester documentation built on Sept. 17, 2021, 8:54 a.m.