Prepping to be RAD

A new fileset was just published that provides new insights into Olympia oyster genomics.

Facilitating analysis of genomic variation in Olympia oysters
Mackenzie Gavery. figshare
http://dx.doi.org/10.6084/m9.figshare.654049

This along with other filesets from FISH546 are featured at oystergen.es/fish546

This dataset includes genomic intervals (BED format) to facilitate RADSeq design and functional annotation of SNPs in Olympia oysters (Ostrea lurida). 

The files include a transcriptome (FASTA format) and the following 8 genomic interval files (BED format):

Oly_snps_bed: location of SNPs with variant annotated in the name column
Oly_geneID_bed: these intervals cover the entire length of the transcript and are annoated with the SwissProt ID in the name column
Oly_regionofblasthits_bed: these intervals cover only the region of homology between the subject and query for the blastx output
Oly_inducible_bed: these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: cell-cell signaling, signal transduction, cell adhesion, development, stress response
Oly_housekeeping_bed: these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: DNA metabolism, RNA metabolism, protein metabolism
Oly_EcoRIsites_bed: location of EcoRI restriction sites
Oly_NotIsites_bed: location of NotI restriction sites
Oly_SbfI_bed: location of SbfI restriction sites

This dataset was generated as part of the requirements for FISH 546: Bioinformatics for Environmental Science.  The slides for the final presentation are included (FISH546.pdf)