Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? ...

• Main Authors: Deagle, Bruce E., Thomas, Austen C., Shaffer, Amanda K., Trites, Andrew W., Jarman, Simon N.
• Format: Dataset
• Language: English
• Published: Dryad 2013
• Subjects: Captive Populations; Diet Analysis; Phoca vitulina
• Online Access: https://dx.doi.org/10.5061/dryad.953hv; https://datadryad.org/stash/dataset/doi:10.5061/dryad.953hv

A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals’ diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify ... : Ion Torrent diet dataFASTQ sequence files and additional data described in the ReadMe file1 MER paper functionsFunctions needed to run R code2 MER R code databaseR code3 MER R code summaryR code ...