Commit 20322084 authored by lbenestan's avatar lbenestan 💬
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Update README.md

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......@@ -33,18 +33,20 @@ We can extract mitochondrion genome sequence from nuclear genome sequence.
# Designing mitochondrial baits
We will consider the 2 mitochondrial genomes available in NCBI (see behind).
Baits will be designed as 180 base pairs length, spread across the entire mitochondrial genome (no overlapping sequences as no need for a mitochondrial assembly).
As the mitochondiral genome of Rana temporaria is about 16,000 bp, a total of about 90 baits will be designed.
We will synthetize the baits using a new technology for de-novo DNA synthesis available in [TWIST](https://www.twistbioscience.com/). We will be receive the baits in one unique tube containing all.
We will consider the two mitochondrial genomes available in NCBI (see behind).
We will target less conservative regions in both intragenic and coding genes.
Baits will be designed as **180 base pairs length**, spread across the entire mitochondrial genome (no overlapping sequences as no need for a mitochondrial assembly).
As the mitochondiral genome of ***Rana temporaria*** is about 16,000 bp, a total of about **90 baits will be designed**.
We will synthetize the baits using a new technology for de-novo DNA synthesis available in [TWIST](https://www.twistbioscience.com/).
We will be receive the baits in one unique tube.
# Hybridization baits and sequencing
Baits will be received as DNA but will be soon transformed in RNA based on the same step fo the hyRAD protocol.
Hybridation will allow 5 to 10% of divergence between the read and the baits sequence, allowing 9 SNPs per sequence at the maximum.
Baits will be received as DNA but will be soon transformed in RNA (to facilitate the hybridization) based on the same step described in the hyRAD protocol.
Hybridation will allow **5 to 10% of divergence** between the DNA and the baits sequence, allowing 9 SNPs per sequence captured at the maximum.
Specificity of baits will be adjusted regarding the temperature of the hybridization.
The removal of non **Rana temporaria** sequences will be done by a post informatics treatment and by sequencing on Miseq our eDNA samples, to ensure about what kind of sequences we have).
The removal of non ***Rana temporaria*** sequences will be done by a post informatic treatment and by sequencing on Miseq our eDNA samples, to screen for other species present in the eDNA sample.
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