This webpage serves to provide additional information, tutorials, and address feedback regarding the FigShare file set co-published with the manuscript: Gavery MR, Roberts SB. (2013) Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc. PeerJ 1:e215 http://dx.doi.org/10.7717/peerj.215
All files are associated with a MBD BS-seq effort targeting Crassostrea gigas gill tissue. Specific files include:
BiGill_CpG_methylation.igv - Location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage.
BiGill_exon_clc_rpkm.igv - Exon-specific gene expression values (RPKM) from RNA-seq analysis.
BiGill_igv_charlie.xml - A session file, which loads methylation and RNA-seq feature tracks as well as the location of C.gigas genome features.
Query to derive_CG_AllData_IGV.txt - Query (SQLShare) used to derive the methylation feature track from the original methratio output (http://goo.gl/5LGq9Q)
These data are developed to be easily visualized in the Integrative Genomics Viewer (IGV). I would suggest installing the downloadable version available here. When you open IGV you should see a browser window as shown.
- Go to File > Load from url
Then your browser should look like…