Facilitating analysis of genomic variation in Olympia oysters

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) The original data for the transcriptome, blastx annotations and SNP tables can be found here: Transcriptome characterization of the Olympia oyster and pinto abalone. Steven Roberts, Emma Timmins-Schiffman. figshare. dx.doi.org/10.6084/m9.figshare.156431. Retrieved 18:14, Mar 18, 2013 (GMT)