Data availability
The pipeline scripts used for this study are available at:
https://github.com/thomasvangurp/epiGBS, with a bug‐fix modification
(https://github.com/MWSchmid/epiGBS_Nov_2017_fixed). The raw sequence
data files for epiGBS (Illumina paired end reads), and for RNAseq
(individual samples’ Illumina paired end reads after quality trimming)
have been submitted to the Sequence Read Archive (SRA) of NCBI under
project number PRJNA790924. The barcodes (barcodes.tsv) required to
process the raw epiGBS sequencing data available on SRA, the reference
contigs (de_novo_contigs.fasta.gz), the annotation of the reference
contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation
data (methylation.txt.gz), and the de novo transcriptome assembly
(de_novo_transcriptome.fasta.gz) are available on zenodo (doi:
10.5281/zenodo.5776915).