Question: How to download BAM file from VM
0
gravatar for nickhir
12 days ago by
nickhir10
german research cancer center (DKFZ)
nickhir10 wrote:

Hey everybody,

I am currently trying to download a BAM file, which is located on a VM to which I am connected over ssh (I want to look at the reads with IGV).

Initially the download is reasonably fast (~7Mb/s), but after a while it goes down to (100kb/s) which means that the download takes over one day...

My question is, if you guys have also encountered a similar problem and if you have an idea how to circumvent this problem. I am using WinScp to download the file.

Any help is much appreciated!

Thanks

download bam vm • 51 views
ADD COMMENTlink written 12 days ago by nickhir10
1

I want to look at the reads with IGV

You can do that directly from the VM itself. Install IGV there. You will need a X11 server locally to receive the X-windows data that will be projected back to your local machine from the VM. MobaXTerm is a free windows program that will provide that functionality.

ADD REPLYlink written 12 days ago by genomax85k
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