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.
logspline object (created with
specifying the empirical density of fragment lengths in the 7 GEUVADIS
't Hoen PA, et al (2013): Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nature Biotechnology 31(11): 1015-1022.
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