Question: Host bam file on MongoDB?
0
gravatar for I0110
2.1 years ago by
I0110120
United States
I0110120 wrote:

Is it possible to host a bam file on MongoDB and slice it with R? I am thinking to develop a shiny app to visualize RNAseq reads for my data. Thanks!

R mongodb • 782 views
ADD COMMENTlink written 2.1 years ago by I0110120

why storing a bam in a database when you can have a direct access to the files on your server ?

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum122k

I want to make a shiny app to visualize a unique type of RNAseq results. Some characters of this RNAseq data cannot be visualized with IGV. I do it with R on my Mac (wouldn't have a server for few months), but it would be a lot easier for my collaborators if it is in a shiny app.

ADD REPLYlink written 2.1 years ago by I0110120
1

it doesn't answer my question: why would you store a BAM in a mongdb when you can store the BAM files on your server ? Storing the path on mongo is OK, storing the reads looks weird to me. see also: In-place writable BAM files

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum122k

How could I store the BAM on my server if I do not have one? As I said I would not have server access for few months :-( Even I have a server, I think MongoDB is more stable and it is free in some cases. Thanks for the link. I will think about it :-)

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by I0110120

How could I store the BAM on my server if I do not have one?

i don't understand; if you have a mongdb server, then you have a server.... (?)

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum122k

If I have a mlab account, can I consider that my server?

ADD REPLYlink written 2.1 years ago by I0110120

ah, I understand now. You're not the owner of the server and your'e just using mongodb as a service.

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum122k
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