Genomic features were developed and reported elsewhere (Gavery and
Roberts 2013). Putative promoters were defined as 1kb regions upstream from
transcription start sites. Transposable elements were identified using RepeatMasker, a
program that screens and annotates interspersed repeats (Smit et al., 1996-2010).
Specifically, RepeatProteinMask, was used with Repbase (Jurka et al. 2005), which
contained 7,445 sequences. Sequence similarities from RepeatProteinMask were
examined using WU-Blast (Lopez et al., 2003) to identify transposable elements which
were included in the genome feature track. A total of 58,468 transposable elements
identified based on sequence similarity. This genome feature track along with intron,
exon, and promoter region feature track are all available via the IPython notebook that
provides code and data used in this manuscript (Olson and Roberts, 2014b). A Chisquared
test was performed to determine if the distribution of differentially methylated
loci among genomic regions (intron, exon, promoter region, transposable elements) was
significantly different to the distribution of all CpGs in the oyster genome
Genomic features were developed and reported elsewhere (Gavery and Roberts 2013). Putative promoters were defined as 1kb regions upstream from transcription start sites. Transposable elements were identified using RepeatMasker, a program that screens and annotates interspersed repeats (Smit et al., 1996-2010). Specifically, RepeatProteinMask, was used with Repbase (Jurka et al. 2005), which contained 7,445 sequences. Sequence similarities from RepeatProteinMask were examined using WU-Blast (Lopez et al., 2003) to identify transposable elements which were included in the genome feature track. A total of 58,468 transposable elements identified based on sequence similarity. This genome feature track along with intron, exon, and promoter region feature track are all available via the IPython notebook that provides code and data used in this manuscript (Olson and Roberts, 2014b). A Chisquared test was performed to determine if the distribution of differentially methylated loci among genomic regions (intron, exon, promoter region, transposable elements) was significantly different to the distribution of all CpGs in the oyster genome