Data from: "White-tailed deer (Odocoileus virginianus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 June 2013-31 July 2013

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Trimmed Un-mapped Data assembly
Downloaded 18 times
Description Resultant BAM file from a pool of rRNA-depleted, non-normalized cDNA of six white-tailed deer from the University of Saskatchewan's Specialized Livestock Research Facility that was assembled de novo in CLC Genomics Workbench 6.0.1.
Download Trimmed Un-mapped Data assembly.bam (1.067Gb)
Details View File Details
Title BLAST results
Downloaded 37 times
Description Top BLAST results of consensus contigs extracted from the .bam file. blastx+ 2.2.27 was used with an e-value threshold of 0.000001 against a custom database of RefSeq eutherian protein sequences.
Download blast.txt (1.542Mb)
Details View File Details
Title dbSNP ss Accession Numbers
Downloaded 13 times
Description List of SNP ss accession numbers detected in the assembly using CLC Genomics Workbench 6.0.1. These SNPs will be available online in the next dbSNP update, currently scheduled for Oct. 2013.
Download Malenfant_04_05_2013.vcf.reformatted.loaded.rep.txt (2.452Mb)
Details View File Details
Title White-tailed deer SNPs (VCF file)
Downloaded 15 times
Description We detected SNPs using CLC’s quality-based variant detection algorithm (min. average quality of five flanking bases on either side of SNP = 15; min. quality of central base = 20; min. coverage = 20; max. coverage = 1000; min. variant frequency = 15%; min. variant count = 4), discarding all reads with non-specific alignments. Multiallelic SNPs were discarded as they may result from incorrect alignment of reads from paralogous genes in the transcriptome data. All SNPs have been submitted to dbSNP and will be available online in the October 2013 update. This VCF file is available in the interim.
Download wtd_SNPs.vcf.txt (3.697Mb)
Details View File Details

When using this data, please cite the original publication:

Genomic Resources Development Consortium, Bensch S, Coltman DW, Davis CS, Hellgren O, Johansson T, Malenfant RM, Moore SS, Palinauskas V, Valkiūnas G (2014) Genomic Resources Notes accepted 1 June 2013 – 31 July 2013. Molecular Ecology Resources 14(1): 218. http://dx.doi.org/10.1111/1755-0998.12166

Additionally, please cite the Dryad data package:

Malenfant R, Davis C, Moore S, Coltman D (2013) Data from: "White-tailed deer (Odocoileus virginianus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 June 2013-31 July 2013. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.79kh0
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Related Data Packages