empirical_density: Estimated distribution of fragment lengths

In polyester: Simulate RNA-seq reads

Description

Empirical fragment length distribution was estimated using 7 randomly selected RNA-seq samples from the GEUVADIS dataset ('t Hoen et al 2013). One sample was selected from each of the 7 laboratories that performed the sequencing. We used Picard's "CollectInsertSizeMetrics" tool (http://broadinstitude.github.io/picard/), version 1.121, to estimate the fragment size distribution based on read alignments. Code we used to estimate this distribution is available at https://github.com/alyssafrazee/polyester/blob/master/make_fraglen_model.R.

Format

logspline object (created with logspline) specifying the empirical density of fragment lengths in the 7 GEUVADIS samples.

References

't Hoen PA, et al (2013): Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nature Biotechnology 31(11): 1015-1022.

polyester documentation built on Nov. 8, 2020, 8:09 p.m.