Data from: Sequence capture of ultraconserved elements from bird museum specimens

McCormack JE, Tsai WLE, Faircloth BC

Date Published: September 16, 2015

DOI: http://dx.doi.org/10.5061/dryad.qh8sh

 

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Title trinity-assemblies-for-dryad.tar.gz
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Description Raw reads assembled de novo into contigs using trinity (trinityrnaseq_r2013-02-25).
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Title toepad-taxa.conf
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Description The taxon-names configuration file for creating UCE data sets for use with the get_match_counts.py (https://github.com/faircloth-lab/phyluce).
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Title toepad-taxa-COMPLETE.tar.gz
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Description Untrimmed and trimmed Nexus files, PHYLIP concatenated alignment, and RAxML input/output for the 100% complete data matrix.
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Title toepad-taxa-COMPLETE-RAxML_bipartitions.FINAL.tre
Downloaded 7 times
Description Newick-formatted tre file for the 100% complete concatenated matrix.
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Title toepad-taxa-INCOMPLETE.tar.gz
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Description Untrimmed and trimmed Nexus files, PHYLIP concatenated alignment, RAxML input/output for the incomplete data matrix. Includes directory of coverage computations for all UCE loci as well as loci in 75% complete data matrix.
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Title toepad-taxa-INCOMPLETE-RAxML_bipartitions.FINAL
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Description Newick-formatted tre file for the 75% complete concatenated matrix.
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Title wesj-103135-reference-sequence.tar.gz
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Description Quasi-reference sequence and sequences indexes for LACM-103135. Used for SNP-calling.
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Title wesj-toepads-realigned.bam.placeholder
Downloaded 23 times
Description Merged BAM file that we realigned around indels using GATK. Contains alignment information for all individuals across which we called SNPs using GATK.
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Title wesj-toepads-rawSNPS-Q30.vcf.gz
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Description Raw SNP calls output by GATK (i.e., not filtered using VariantFiltration).
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Title wesj-toepads-inDels-Q30.vcf.gz
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Description InDel calls using for VariantFiltration in GATK.
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Title wesj-toepads-Q30-QD2-LOW-STRICT.vcf.gz
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Description Filtered raw SNP data (i.e., these have been put through VariantFiltration).
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Title Q30-QD2-MISS_0.75.recode.vcf.gz
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Description Filtered SNPs that have undergone VariantFiltration and also selection for presence in 75% of individuals genotypes. SNPs in this file have further been filtered for the presence of informative sites.
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Title Q30-QD2-MISS_0.75.recode.snapp.nexus.gz
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Description Filtered SNPs that have undergone VariantFiltration and also selection for presence in 75% of individuals genotypes. SNPs in this file have further been filtered for the presence of informative sites. SNPs in this file have been re-formatted for SNAPP, and this file contains data for individuals USNM-144749 and MLZ-59834, which we removed from the data set prior to analysis.
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Title Structure_infile_SNPS_jays.txt.gz
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Description Filtered SNPs that have undergone VariantFiltration and also selection for presence in 75% of individuals genotypes. SNPs in this file have further been filtered for the presence of informative sites. Finally, SNPs in this file have been re-formatted for STRUCTURE.
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Title SNAPP_analysis.tar.gz
Downloaded 6 times
Description Input files prepared for SNAPP and output files generated by SNAPP. The WESJ_SNAPP_TIPS_ed.xml input file created for SNAPP *does not* contain data for individuals USNM-144749 and MLZ-59834, which we removed from the data set prior to analysis.
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Title Structure_Results_SNPs_jays.tar.gz
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Description Output files generated by STRUCTURE.
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Title toepad-taxa.ProcessingSteps.DRYAD.txt
Downloaded 75 times
Description Processing steps we used for analysis of these data.
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Title SRA-locations.txt
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Description Locations of raw sequence read files in the NCBI SRA.
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When using this data, please cite the original publication:

McCormack JE, Tsai WLE, Faircloth BC (2016) Sequence capture of ultraconserved elements from bird museum specimens. Molecular Ecology Resources 16(5): 1189–1203. http://dx.doi.org/10.1111/1755-0998.12466

Additionally, please cite the Dryad data package:

McCormack JE, Tsai WLE, Faircloth BC (2015) Data from: Sequence capture of ultraconserved elements from bird museum specimens. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.qh8sh
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