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ropensci / biomartr

Genomic Data Retrieval with R
https://docs.ropensci.org/biomartr
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Question about downloading mitochondrial genomes #47

Open ucbtmae opened 4 years ago

ucbtmae commented 4 years ago

Dear author,

Thanks and cheers for developing this package!

I have the question as to how to use the package to download complete mitochondrial genomes from the NCBI. This is because I am going to working with DNA metabarcoding, and I am interested in developing some new primer pairs for certain animal groups.

I have seen that there are some types that we can specify in the code such as "cds" or "rna", but I haven't seen the option for mitochondrial DNA

Best regards!

HajkD commented 4 years ago

Hi,

Many thanks for contacting me.

Could you please provide an example file/link from/to NCBI?

So far, I haven't implemented this functionality yet, but given an example file, I am happy to see what I can do.

Many thanks!

ucbtmae commented 4 years ago

Hi!

Sorry for the very late response!

I am attaching one link to one example file on NCBI

https://www.ncbi.nlm.nih.gov/nuccore/NC_015079.1

The idea is to batch download complete mitochondrial genomes so it would be possible to explore them by groups (insect, reptiles, fish) to design new metabarcoding primers for eDNA studies.

Thanks again for all your support!

Best regards

HajkD commented 4 years ago

Hi,

Thank you for providing this example.

I put it on my TODO list now and will start working on this new feature.

Many thanks!