Commit d55a1a69 authored by lbenestan's avatar lbenestan 💬
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Update README.md

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......@@ -31,3 +31,22 @@ We can extract mitochondrion genome sequence from nuclear genome sequence.
* No mitochondrion extracted from **UCB_Rtem_1**
* :exclamation: **UCB_Rtem_1** illumina raw reads necessary to extract mitogenome are not available https://www.ncbi.nlm.nih.gov/Traces/wgs/VIAC01
# 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 target less conservative regions in both intragenic and coding genes.
# 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.
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).
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