and the 9 contigs that were not anchored on the 19 super-scaffolds. 196,214,630 sites were retained after the above steps. SNP calling was then conducted using Freebayes54to call sites with Quality >20. We performed several filtering steps to minimize SNP calling...
One limitation of our study is that, without a ChIP-grade antibody, we must overexpress the TF fused with an epitope tag to perform ChIP-seq, making it difficult to control for protein level, as well as where and when the TF is expressed. Since ChIP-seq is an enrichment analysis, factor...