title: Double-digest RAD-Seq of American Crows (Corvus brachyrhynchos): Muscle and blood
design: We generated reduced representation double digest restriction-associated DNA (ddRAD) libraries from blood and frozen tissue samples. We followed the ddRAD sequencing protocol of Peterson et al. (2012). We digested 350-500 ng of DNA with SbfI-HF and MspI rriction endonucleases (New England BioLabs, Ipswich, MA), pooled sets of 8 samples, and size-selected 415-515 bp DNA fragments on a BluePippin machine (Sage Science, Beverly, MA). We multiplexed 96 avian ddRAD libraries from this study and another study, obtaining two runs of single-end 50-bp reads from Illumina HiSeq 2500 at the Computational Genomics Research Laboratory at the University of California (Berkeley, CA). We used process_radtags in STACKS 1.42 (Catchen et al. 2013) with default settings to demultiplex reads, discard low-quality reads, discard reads with an uncalled base, rescue barcodes, and rescue SbfI RAD tags.
identifiers.namespace: SUB6698398
identifiers.id: nf01