Data from: Accuracy of allele frequency estimation using pooled RNA-Seq

Konczal M, Koteja P, Stuglik MT, Radwan J, Babik W

Date Published: October 11, 2013

DOI: http://dx.doi.org/10.5061/dryad.bh23t

 

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 hq_SNPs_and_estimation_error_calculations
Downloaded 29 times
Description This file contains high quality SNPs selected for allele frequency estimation and comparison between individual genotypes and pool frequencies. We present here numbers of reads of reference and alternative variants and calculations of relative estimation errors.
Download hq_SNPs_and_estimation_error_calculations.txt (2.480 Mb)
Details View File Details
Title Bank_vole_reference_transcriptome_liver
Downloaded 15 times
Description The bank vole liver reference transcriptome
Download C3W_final_transcriptome.fasta (106.5 Mb)
Details View File Details
Title Contigs_9het
Downloaded 5 times
Description Contigs probably representing pairs of paralogs
Download Contigs_9het.txt (1.309 Kb)
Details View File Details
Title var.flt.ind.default
Downloaded 5 times
Description File with SNPs called from 10 unrelated individuals from one line of laboratory colony.
Download var.flt.ind.default.vcf (87.00 Mb)
Details View File Details
Title var.flt.pool.flat
Downloaded 6 times
Description File with SNPs called from one sample consisting of 10 bank vole individuals
Download var.flt.pool.flat.vcf (39.37 Mb)
Details View File Details
Title Expression_level_ind_pooled_mean
Downloaded 35 times
Description Expression level values for ten individual samples and one pool consisting of the same individuals; calculations of relative estimation errors
Download transcript_ind_pooled_mean.xlsx (2.699 Mb)
Details View File Details
Title genotypes_default_Q30_dp5_q30
Downloaded 8 times
Description Genotypes of 10 individuals for high quality SNPs. Tab delimited file
Download genotypes_default_Q30_dp5_q30.txt (1.759 Mb)
Details View File Details
Title Ind_reads_counts
Downloaded 2 times
Description File with number of reads with given variant for 10 individuals for high quality SNPs
Download ind.sync (3.626 Mb)
Details View File Details
Title python_scripts
Downloaded 41 times
Description Python scripts used for VCF files filtering, Fst simulations and allele specific gene expression assesment.
Download python_scripts.zip (10 Kb)
Details View File Details

When using this data, please cite the original publication:

Konczal M, Koteja P, Stuglik MT, Radwan J, Babik W (2014) Accuracy of allele frequency estimation using pooled RNA-Seq. Molecular Ecology Resources 14(2): 381-392. http://dx.doi.org/10.1111/1755-0998.12186

Additionally, please cite the Dryad data package:

Konczal M, Koteja P, Stuglik MT, Radwan J, Babik W (2013) Data from: Accuracy of allele frequency estimation using pooled RNA-Seq. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.bh23t
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: