Data from: Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

Graham CF, Glenn TC, McArthur AG, Boreham DR, Kieran T, Lance S, Manzon RG, Martino JA, Pierson T, Rogers SM, Wilson JY, Somers CM

Date Published: March 18, 2015

DOI: http://dx.doi.org/10.5061/dryad.mf1ck

 

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Title RadtagCounter
Downloaded 18 times
Description Perl script that counts the number of RADtags in each*.matches file within a directory
Download RadtagCounter.pl (1.043 Kb)
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Title SNPCounter
Downloaded 8 times
Description Counts the number of potential variable sites in a .vcf file generated by populations in the stacks program
Download SNPCounter.pl (1.914 Kb)
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Title genotypecounter.pl
Downloaded 6 times
Description perl script to determine how many genotype calls within the same individual are the same as the 0 hour muscle call
Download genotypecounter.pl (3.342 Kb)
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Title compressposition.pl
Downloaded 6 times
Description perl script to remove multiple entries for a variable site position and determine the total coverage of each position
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Title coveragecounter.pl
Downloaded 4 times
Description perl script to determine if a call in the 12, 48 or 96 file is present in the 0 file and if it is it determines the coverage at that position. The output is the average coverage per snp position
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Title AdapterInfo
Downloaded 31 times
Description This file contains the internal and external adapters for each sample as well as the reverse compliment for the i7 tags.
Download AdapterInfo-v2.xlsx (51.70 Kb)
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Title D1FastqFiles
Downloaded 10 times
Description Fastq files for the first restriction enzyme pair, EcoRI-NheI
Download D1FastqFiles.tar.gz (5.826 Gb)
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Title D2FastqFiles
Downloaded 11 times
Description Fastq files for the second restriction enzyme pair, EcoRI-ClaI
Download D2FastqFiles.tar.gz (4.831 Gb)
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Title SamplingInfo
Downloaded 44 times
Description File containing the treatment time, tissue type and restriction enzyme pair of each sample
Download SamplingInfo.xlsx (49.65 Kb)
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When using this data, please cite the original publication:

Graham CF, Glenn TC, McArthur AG, Boreham DR, Kieran T, Lance S, Manzon RG, Martino JA, Pierson T, Rogers SM, Wilson JY, Somers CM (2015) Impacts of Degraded DNA on Restriction Enzyme Associated DNA (RAD) Sequencing. Molecular Ecology Resources 15(6): 1304–1315. http://dx.doi.org/10.1111/1755-0998.12404

Additionally, please cite the Dryad data package:

Graham CF, Glenn TC, McArthur AG, Boreham DR, Kieran T, Lance S, Manzon RG, Martino JA, Pierson T, Rogers SM, Wilson JY, Somers CM (2015) Data from: Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.mf1ck
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