Raw fragment counts of RNA sequencing from single oocytes
Pair end sequencing data were produced from five single oocytes following the procedures described in Biase (2021). Sequences were aligned with Hisat2 (Kim et al., 2015; Kim et al., 2019; Pertea et al., 2016), followed by filtering with samtools (Li et al., 2009) (remove unmapped reads, secondary alignments, failing of platform quality checks, PCR or optical duplicate) and removal of duplicates with the function ‘bammarkduplicates’ from biobambam (Tischler and Leonard, 2014). Sorting and indexing were done with Picard (http://broadinstitute.github.io/picard/). Finally, fragments were counted with ‘featurecounts’ (Liao et al., 2014) using the Ensembl (Flicek et al., 2014; Kinsella et al., 2011) bovine annotation as a guide.