Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans

Viricel A, Pante E, Dabin W, Simon-Bouhet B

Date Published: November 21, 2013

DOI: http://dx.doi.org/10.5061/dryad.mk364

 

Files in this package

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Title Description of files deposited to Dryad
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Description Description of files deposited to Dryad
Download Dryad_File_descriptions.txt (1.974 Kb)
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Title R script: 1_Slacks
Downloaded 22 times
Description This script allows testing multiple values for two stacks parameters used in the denovo_map command: M and n. It runs both denovo_map and populations commands.
Download 1_Slacks.R (1.269 Kb)
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Title R script: 2_RAD_Parse_tags
Downloaded 15 times
Description This script was used to retrieve and sort sequences from the stacks outputs (after applying the populations command) into variable versus invariable sequences. These sequences were then blasted using Blast2GO.
Download 2_RAD_Parse_tags.R (2.368 Kb)
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Title R script: 3_RAD_Similarity_evalue_blastn
Downloaded 12 times
Description This script retrieves the similarity scores from Blast results obtained using Blast2GO, calculates the median and range, and builds a histogram of these similarity values.
Download 3_RAD_Similarity_evalue_blastn.R (1.995 Kb)
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Title R script: 4_RAD_Parse_blast_xml_Pp_Dd
Downloaded 22 times
Description This script was used to summarize Blast hits results from Blast2GO (number of hits belonging to each organism) and to retrieve and export in fasta format the whole sequence from the best hits (these longer sequences were subsequently used in Blast2GO).
Download 4_RAD_Parse_blast_xml_Pp_Dd.R (5.953 Kb)
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Title R script: 5_Getting_info_on_best_Ttru_hit_sequences
Downloaded 10 times
Description This script retrieves the length of the best Blast hit sequences obtained using the previous R script.
Download 5_Getting_info_on_best_Ttru_hit_sequences.R (808 bytes)
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Title R script: 6_Annotation_analysis_DelphinusTursiops_RADtag_08-13-2013
Downloaded 17 times
Description This script was used to make histograms of the Blast2GO annotation results.
Download 6_Annotation_analysis_DelphinusTursiops_RAD...13.R (2.745 Kb)
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Title sequence file for individual 9902012
Downloaded 9 times
Description Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
Download 9902012.fq (304.2 Mb)
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Title sequence file for individual 10201010
Downloaded 7 times
Description Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
Download 10201010.fq (436.9 Mb)
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Title sequence file for individual 10307073
Downloaded 5 times
Description Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
Download 10307073.fq (334.9 Mb)
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Title sequence file for individual 10401011
Downloaded 5 times
Description Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
Download 10401011.fq (383.0 Mb)
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Title sequence file for individual 10512077
Downloaded 7 times
Description Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
Download 10512077.fq (433.9 Mb)
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Title sequence file for individual 10712131
Downloaded 5 times
Description Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
Download 10712131.fq (509.5 Mb)
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Title Stacks_commands
Downloaded 21 times
Description Three stacks commands: process_radtags, denovo_map, populations.
Download Stacks_commands.txt (780 bytes)
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Title Blast2GO annotation results
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Description This file contains annotation results from Blast2GO.
Download All_annotation_results_08-13-2013.csv (623.9 Kb)
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Title xml output file from Blast2GO for conserved tags
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Download blastResult_blastn_conserved.xml (14.95 Mb)
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Title xml output file from Blast2GO for variable tags
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Download blastResult_blastn_variable.xml (20.05 Mb)
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Title xml output file from Blast2GO for conserved tags: Tursiops hits
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Download blastResult_blastx_conserved_best_Ttru_hits.xml (11.55 Mb)
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Title xml output file from Blast2GO for variable tags: Tursiops hits
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Download blastResult_blastx_variable_best_Ttru_hits.xml (18.94 Mb)
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Title Blast2GO result (blastn) for conserved tags: Evalues
Downloaded 11 times
Download Evalue_blastn_conserved_chart_data_201307...51.txt (231 bytes)
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Title Blast2GO result (blastn) for variable tags: Evalues
Downloaded 13 times
Download Evalue_blastn_variable_chart_data_2013071...51.txt (232 bytes)
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Title Blast2GO result (blastn) for conserved tags: Similarity values
Downloaded 7 times
Download Similarity_blastn_conserved_chart_data_20...37.txt (182 bytes)
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Title Blast2GO result (blastn) for variable tags: Similarity values
Downloaded 10 times
Download Similarity_blastn_variable_chart_data_201...36.txt (192 bytes)
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When using this data, please cite the original publication:

Viricel A, Pante E, Dabin W, Simon-Bouhet B (2013) Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans. Molecular Ecology Resources 14(3): 597–605. http://dx.doi.org/10.1111/1755-0998.12206

Additionally, please cite the Dryad data package:

Viricel A, Pante E, Dabin W, Simon-Bouhet B (2013) Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.mk364
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