Data from: EpiRADseq: scalable analysis of genome-wide patterns of methylation using next-generation sequencing

Schield DR, Walsh MR, Card DC, Andrew AL, Adams RH, Castoe TA

Date Published: July 7, 2015

DOI: http://dx.doi.org/10.5061/dryad.hs200

 

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Title Daphnia ambigua epiRADseq Pseudo-reference Genome
Downloaded 9 times
Description The pseudo-reference genome was constructed using all epiRAD reads, which was used for read mapping and inferring methylation. This file is in fasta format and is compressed.
Download Daphnia_ambigua_EpiRADseq_Reference.fasta.bz2 (948.9 Kb)
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Title Daphnia ambigua epiRADseq Mapping Output Files
Downloaded 11 times
Description A zipped archive containing BAM mapping files for each sample (3 replicates across 2 treatments) mapped to the Daphnia ambigua pseudo-reference genome.
Download Daphnia_ambigua_EpiRADseq_Mapping_Files.tar.bz2 (144.8 Mb)
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Title Daphnia ambigua EpiRADseq Raw Count Tables
Downloaded 3 times
Description A zipped archive containing the raw counts for each sample (3 replicates across 2 treatments) derived from the mapping to the Daphnia ambigua pseudo-reference genome. The four columns (in order) are: (1) The reference sequence/contig ID, (2) The length of the sequence/contig, (3) The number of reads that mapped to the sequence/contig, and (4) the number of reads that didn't map to the sequence/contig.
Download Daphnia_ambigua_EpiRADseq_Raw_Counts.tar.bz2 (427.8 Kb)
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Title Daphnia ambigua P treatment - first generation with predatory cues treatment (3 replicates) - Raw Illumina Reads
Downloaded 25 times
Description A zipped fastq file that contains multiplexed reads from the three replicates from the predator treatment (generation 1). A script within the Data_processing_scripts.tar.bz archive will automatically perform the parsing using a barcodes file located in that same archive. These replicates are referred to as the P treatments in the manuscript and with all applicable Dryad file names and processing steps.
Download P_Gen1_Predator_Treatment.fastq.bz2 (239.7 Mb)
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Title Daphnia ambigua PN treatment - second generation without predatory cues treatment (3 replicates) - Raw Illumina Reads
Downloaded 7 times
Description A zipped fastq file that contains multiplexed reads from the three replicates from the no predator treatment (generation 2). A script within the Data_processing_scripts.tar.bz archive will automatically perform the parsing using a barcodes file located in that same archive. These replicates are referred to as the PN treatments in the manuscript and with all applicable Dryad file names and processing steps.
Download PN_Gen2_NoPredator_Treatment.fastq.bz2 (163.7 Mb)
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Title Frequency summary of Daphnia pulex genome double digest
Downloaded 6 times
Description A summary file that provides the number of fragments in given fragment size range. Based on an in silico digestion of the Daphnia pulex genome. The Perl script used to generate this data is contained with all other data processing scripts.
Download Daphnia_pulex_summary_doubleDigest_CTGCAG_CCGG.txt (538 bytes)
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Title Daphnia ambigua EpiRADseq Data Analysis Scripts, Files, & Documentation
Downloaded 23 times
Description A zipped archive containing all scripts necessary to quality-trim raw reads, construct the pseudo-reference genome, and map the reads back to the psuedo-reference to infer methylation. Each script contains a proper description of function and usage and the complete pipeline (from raw reads to counts) is automated and documented in the EpiRADseq_analysis.sh script.
Download Data_processing_scripts.tar.bz2 (7.636 Kb)
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Title Daphnia ambigua EpiRADseq Rarefaction Raw Read Files
Downloaded 8 times
Description A zipped archive containing randomly subsetted read files from all replicates, which were used for rarefaction analysis.
Download Rarefaction_Daphnia_ambigua_EpiRADseq_Raw...ar.bz2 (75.31 Mb)
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Title Daphnia ambigua EpiRADseq Rarefaction Mapping Files
Downloaded 7 times
Description A zipped archive containing BAM mapping files for each rarefacted sample (3 replicates across 2 treatments) mapped to the Daphnia ambigua pseudo-reference genome.
Download Rarefaction_Daphnia_ambigua_EpiRADseq_Map...ar.bz2 (89.34 Mb)
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Title Daphnia ambigua EpiRADseq Rarefaction Raw Count Tables
Downloaded 7 times
Description A zipped archive containing the raw counts for each rarefacted sample (3 replicates across 2 treatments) derived from the mapping to the Daphnia ambigua pseudo-reference genome. The four columns (in order) are: (1) The reference sequence/contig ID, (2) The length of the sequence/contig, (3) The number of reads that mapped to the sequence/contig, and (4) the number of reads that didn't map to the sequence/contig.
Download Rarefaction_Daphnia_ambigua_EpiRADseq_Raw...ar.bz2 (385.8 Kb)
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When using this data, please cite the original publication:

Schield DR, Walsh MR, Card DC, Andrew AL, Adams RH, Castoe TA (2016) EpiRADseq: scalable analysis of genome-wide patterns of methylation using next-generation sequencing. Methods in Ecology and Evolution 7(1): 60-69. http://dx.doi.org/10.1111/2041-210X.12435

Additionally, please cite the Dryad data package:

Schield DR, Walsh MR, Card DC, Andrew AL, Adams RH, Castoe TA (2015) Data from: EpiRADseq: scalable analysis of genome-wide patterns of methylation using next-generation sequencing. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hs200
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