Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013

 

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Title Custom Perl script for extracting SNPs
Downloaded 40 times
Description Perl program used to extract SNPs. Properly accounts for REFSKIP characters (i.e., "<" and ">") that result from spliced alignments and seemed to be problematic in more widely available SNP calling packages, such as samtools and varscan.
Download getsnpsfrommpileup.pl (8.142 Kb)
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Title SNP VCF file
Downloaded 59 times
Description VCF file containing info for SNPs called using the getsnpsfrommpileup.pl script. Settings used were: coverage >= 10, freq. of minor allele >= 0.2, read support for minor allele >= 3, number of alleles = 2. All SNPs were also verified using the program SysCall, and were retained only if the posterior probability of being a variant was >= 0.95.
Download pb_syscallsnps.vcf.txt (4.097 Mb)
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Title Contig annotation file
Downloaded 34 times
Description Putative gene and gene ontology annotations for transcripts that were deemed to be "full length" (i.e., cover >= 90% of their best blastx hit in RefSeq). These sequences are available on NCBI under the BioProject accession PRJNA193538.
Download annotations.annot (17.75 Mb)
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When using this data, please cite the original publication:

Genomic Resources Development Consortium, Coltman DW, Davis CS, Lunn NJ, Malenfant RM, Richardson ES (2014) Genomic Resources Notes accepted 1 August 2013 – 30 September 2013. Molecular Ecology Resources 14(1): 219. http://dx.doi.org/10.1111/1755-0998.12190

Additionally, please cite the Dryad data package:

Malenfant RM, Coltman DL, Richardson ES, Lunn NJ, Davis CS (2013) Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.606j6
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