@@ -34,7 +34,7 @@ We can extract mitochondrion genome sequence from nuclear genome sequence.
# Designing mitochondrial baits
We considered the two high-quality mitochondrial genomes assemblies available in NCBI, MH536744 and MT483700. Despite being less properly assebmled, a third non-annotated mitocondrion sequence (LR991693) was included here since it aligned correctly except for two regions of 3500 and 1500 bp.
We targeted the complete mitochondrion genome, including less conservative regions in both intragenic and coding genes. To that end, we run [MAFFT] to align the three above-mentioned mitochondial genomes using Geneious. Positions containing any gaps were masked and removed.
We targeted the complete mitochondrion genome, including less conservative regions in both intragenic and coding genes. To that end, we run MAFFT to align the three above-mentioned mitochondial genomes using Geneious. Positions containing any gaps were masked and removed.
Baits were designed as **180 base pairs length**, spread across the entire mitochondrial genome (no overlapping sequences as no need for a mitochondrial assembly) using [BaitDesigner](https://gatk.broadinstitute.org/hc/en-us/articles/360037069172-BaitDesigner-Picard-). The T7 promoter was added to the 5' end of the baits for later transcription using the [NEB kit E2040S](https://international.neb.com/products/e2040-hiscribe-t7-high-yield-rna-synthesis-kit#Product%20Information). Altogether, there was only one ambiguity character which was simply depreciated.
