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Old 06-25-2012, 10:57 AM   #1
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Default BaseSpace for MiSeq

We did our first real run of bacterial genomes on the MiSeq and thankfully saved data files locally and on the cloud app BaseSpace.

Everything looks good on the MiSeq but the cloud app choked. We found it was missing one *.bcl file. Called Illumina, they have no idea about BaseSpace. We were told to leave the problem on their website as a feature request. We were excited about using BaseSpace as an avenue to share data and allow people to get post FASTQ analysis options. First try is a fail without any clear route to getting a simple problem fixed.

When on the phone I wanted to find out what parameters their canned analysis used, etc. but it seems like BaseSpace is an entirely different group with no support line. It is in Beta...

Anyone have any contact for BaseSpace when problems arise? Sitting on hold at Illumina for 45 mins to be told they don't know anything about it was not very helpful.
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Old 06-25-2012, 11:08 AM   #2
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I will admit upfront that I have no experience with BaseSpace. We analyze MiSeq data with regular CASAVA.

That said:

Can you force a re-sync of the data folder with basespace? If all you are missing is one BCL file then you can get that uploaded easily.

If the BCL file is truely missing (happens sometimes) then see if there is an option to have pipeline go forward with "--ignore-missing-bcl". Not sure if this option exists in BaseSpace, but it does in regular CASAVA.

Last edited by GenoMax; 06-25-2012 at 11:17 AM.
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Old 11-26-2012, 07:24 PM   #3
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Originally Posted by epistatic View Post
Called Illumina, they have no idea about BaseSpace.
My experience exactly. First I was excited about BaseSpace, but it is unclear what you can actually do with it and what not, what the pricing structure will be, and most importantly what the security model of the whole thing is.

I could talk to a guy from Illumina a couple of days ago and tried to ask him about BaseSpace, and he was like "What's BaseSpace?!?"
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Old 11-27-2012, 02:55 AM   #4
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BaseSpace is a gimmick with very little analytical functionality.
Why not just store locally?
After each run you can decide what files you would like to keep permanently based on whether you need to troubleshoot etc.
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Old 11-27-2012, 08:43 AM   #5
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Default we do both

We store locally and in the cloud-mostly so our customers can see the data right away and comment on it.

We pipeline through the regular channels because as of now, BaseSpace doesn't demultiplex the samples.

I know they are adding BaseSpace for HiSeq soon, so maybe if the person spoken to was only on HiSeq they may not know anything about BaseSpace yet.
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Old 11-27-2012, 04:48 PM   #6
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Hi there,...

what do you mean by "BaseSpace doesn't multiplex"? As far as i see it in my projects i can clearly see all different samples demultiplexed and even QC on the multiplexing so i wonder what you are concerned with?

I have to admit BaseSpace is not yet the solution solving all analysis problems but as mentioned it is still in "Beta Phase". Once launched it will come with full support and i am sure you then will get the answers you seek if you have any by the BaseSpace support team.

BaseSpace on the HiSeq will also be available on the full launch, and there is a recent data set that has just been posted on BaseSpace:

Basic analysis will be part of every run, and once the App Store launches it will be a lot more helpful and enabling for non bioinformatics savvy users.

I am sorry you got connected to someone who has never heard of BaseSpace within Illumina, where did you call to get this response? It is common that support is not quite clear yet about features on BaseSpace, that is why there is a special support for BaseSpace which can be easily addressed via BaseSpace itself!

Security wise it is based in the amazon cloud, since people wire and store their money information in that i am sure it is safe enough to host seq data! Pricing schemes are still in development for Apps but the general data storage pricing is already released:

Please shoot me any questions and I am happy to help if i have any infos, but so far i am also waiting on the full release to see what the overall performance will look like!

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