Data from: A linkage map and QTL analysis for pyrethroid resistance in the bed bug Cimex lectularius

Fountain T, Ravinet M, Naylor R, Reinhardt K, Butlin RK

Date Published: October 24, 2016

DOI: http://dx.doi.org/10.5061/dryad.d4r50

 

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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 Remove PCR duplicates
Downloaded 2 times
Description Bash script to remove PCR duplicates using Stacks 1.21 clone_filter module
Download remove_pcr_duplicates.sh (304 bytes)
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Title Align RAD-seq reads
Downloaded 2 times
Description Align RAD-seq reads to bedbug reference genome using GSNAP
Download pair_end_alignment.sh (967 bytes)
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Title Stacks refmap pipeline
Downloaded 11 times
Description Make Stacks catalogue from reference mapped data
Download stacks_refmap.sh (5.204 Kb)
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Title QTL mapping for pyrethroid resistance
Downloaded 14 times
Description Rscript that uses rqt_final_cross.csv to perform qtl mapping for pyrethroid resistance using R/qtl
Download rqtl_mapping.R (5.28 Kb)
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Title Final cross data
Downloaded 6 times
Description Filtered and corrected linkage map data for use in QTL mapping
Download bedbugs_cross_final_100316.csv (83.01 Kb)
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Title Construct linkage map
Downloaded 11 times
Description Rscript for constructing a linkage map from filtered raw data (bedbugs_raw_filtered.csv) using Rqtl
Download make_genetic_map.R (35.40 Kb)
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Title Filtered raw cross data
Downloaded 5 times
Description Genotype data output by Stacks that has been filtered to include loci only informative for QTL and linkage map analysis (i.e. ab/ab in both F1 parents)
Download bedbugs_raw_filtered.csv (131.8 Kb)
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Title Stacks raw genotypes
Downloaded 3 times
Description Raw genotypes from Stacks calling pipeline.
Download stacks_raw_genotypes.tsv (2.078 Mb)
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Title Convert stacks raw output to Rqtl
Downloaded 16 times
Description Utility tool to convert stacks raw output to Rqtl input
Download rqtl_format_conversion.R (2.502 Kb)
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Title Stacks catalogue output
Downloaded 5 times
Description Raw output data from Stacks catalogue - includes alleles, SNPs and RAD tags called from Stacks reference mapping pipeline.
Download stacks_catalogue_output.zip (555.8 Kb)
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When using this data, please cite the original publication:

Fountain T, Ravinet M, Naylor R, Reinhardt K, Butlin RK (2016) A linkage map and QTL analysis for pyrethroid resistance in the bed bug Cimex lectularius. G3: Genes - Genomes - Genetics 6(12): 4059-4066. http://dx.doi.org/10.1534/g3.116.033092

Additionally, please cite the Dryad data package:

Fountain T, Ravinet M, Naylor R, Reinhardt K, Butlin RK (2016) Data from: A linkage map and QTL analysis for pyrethroid resistance in the bed bug Cimex lectularius. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.d4r50
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