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Sequences for BioProject PRJNA431646 not available online #8

Open IgnatiusPang opened 5 years ago

IgnatiusPang commented 5 years ago

Dear Administrator,

I have tried to download the viral mock community (BioProject PRJNA431646) referenced in the VirMap paper. However, to the best of my knowledge it does not seems to be online (e.g. the data is not publically available yet?). If possible, would you please have a look at this for me? Thank you in advance.

Yours Sincerely,

Igy

najami commented 5 years ago

I'll look into it and get back to you.

On Thu, Jul 18, 2019 at 1:32 AM IgnatiusPang notifications@github.com wrote:

Dear Administrator,

I have tried to download the viral mock community (BioProject PRJNA431646) referenced in the VirMap paper. However, to the best of my knowledge it does not seems to be online (e.g. the data is not publically available yet?). If possible, would you please have a look at this for me? Thank you in advance.

Yours Sincerely,

Igy

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QianGuoPKU commented 5 years ago

Hi, I wonder if there is any alternative access to the viral mock community sequence data. The data in NCBI seems to be unavailable still. Thanks.

pcantalupo commented 5 years ago

Maybe some of these might help you:

Good luck

najami commented 5 years ago

NetoVir is a good set and we ran it through VirMAP as well - thanks for suggesting this @pcantalupo. This recent paper also cites a few mock communities and virome datasets:

Sutton, T. D. S., Clooney, A. G., Ryan, F. J., Ross, R. P., & Hill, C. (2019). Choice of assembly software has a critical impact on virome characterisation. Microbiome, 7(1), 12. https://doi.org/10.1186/s40168-019-0626-5

I've contacted NCBI and requested BioProject PRJNA431646 to be made public. I am not sure why this hasn't been public since the paper came out but we'll get it out there so @qianguopku, @IgnatiusPang, and others can use it. Please let me know if there is anything else I can help with in the meantime.

pcantalupo commented 5 years ago

@najami Thank you for the Sutton link!

QianGuoPKU commented 5 years ago

@najami @pcantalupo Thank you.

najami commented 5 years ago

@pcantalupo @IgnatiusPang @qianguopku - we (re)submitted the dataset to SRA. I'll let you know as soon as it is available.

IgnatiusPang commented 5 years ago

Thank you for re-submitting the data!

najami commented 5 years ago

@IgnatiusPang you are welcome!

Here's the direct link in case others are interested: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR9875293