Data delivery for HiSeq

[Sivakumar Gowrisankar]

Hi,

For those of you who are in a core lab, would you please share how you deliver data to your customers? I am especially interested in the HiSeq data.

Thank you
Siva

[Davide Cittaro]

On Oct 7, 2010, at 4:04 PM, Sivakumar Gowrisankar wrote:

> Hi,
>
> For those of you who are in a core lab, would you please share how you deliver data to your customers? I am especially interested in the HiSeq data.
>

We are testing galaxy (http://usegalaxy.org) for that.

d

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Davide Cittaro
daweo...@gmail.com
http://daweonline.googlepages.com/

[Kittler, Ellen Ph. D.]

I'm ordering a blue ray disk burner for off campus users ! On-campus users have a pick up area at nearline storage on the high performance cluster.

Ellie

d

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[Terry Camerlengo]

Depending on specifics....website and/or FTP server.

--

[Chulhong Kim]

Dear Siva
In our case we deliver the seq data to customer using Hdd. If you use the FTP then it spend too much time.
Brst regards.
Chul Kim

2010. 10. 7. 오후 11:04에 "Sivakumar Gowrisankar" <siv...@gmail.com>님이 작성:

--

[aubin thomas]

Hi,

it depends on the type of the files that you want to share. A FTP with secure connection is suitable if you share only the reads that pass the filter

[Ammar Husami]

We use a secure file sharing tool that is only available to cchmc faculty and staff, and we purchased 20GB of space for $50/year. http://bmixythos.cchmc.org
but we can use it to send data inside and outside the organization.

Ammar Husami
Applications Specialist
Molecular Diagnostics Laboratory
Department of Human Genetics
Cincinnati Children's Hospital Medical Center

[Terry Camerlengo]

Why would you say FTP takes too much time? A typical export file compressed is around 7-8 GB per lane. On a network connection around 15 Mbs (the average rates at our institution) you are looking at a download time of 7-10 minutes per lane. 

Not fast by any means, but considering the size of the files, it certainly beats burning things to DVDs and mailing it.

2010/10/7 Chulhong Kim <cybo...@gmail.com>

[Andrew Gagne]

We generally distribute data via ftp, although some of our users request their entire run folder and we transfer that on our internal shared storage system.

andrew

2010/10/7 Terry Camerlengo <terry.ca...@gmail.com>

[Sivakumar Gowrisankar]

Thanks everyone for sharing your views. We personally use a mixture of internal shared storage system data transfer and our LIMS system. We are slowly migrating towards an FTP system and give customer id passwords to account for data privacy.

2010/10/7 Andrew Gagne <aga...@gmail.com>

[rc]

You may want to check out Sample Tracking in Galaxy. It has a neat
data transfer mechanism, where a lab manager can browse and select
datasets and upload them to data libraries in Galaxy from which the
users may later download or analyze them using Galaxy.

Data transfer screencast: http://screencast.g2.bx.psu.edu/sample_tracking/transfer_datasets.html
Sample tracking docs: http://main.g2.bx.psu.edu/u/rkchak/p/sts

thanks
rc

On Oct 8, 12:14 am, Sivakumar Gowrisankar <siv...@gmail.com> wrote:
> Thanks everyone for sharing your views. We personally use a mixture of
> internal shared storage system data transfer and our LIMS system. We are
> slowly migrating towards an FTP system and give customer id passwords to
> account for data privacy.
>
> 2010/10/7 Andrew Gagne <aga...@gmail.com>
>
> > We generally distribute data via ftp, although some of our users request
> > their entire run folder and we transfer that on our internal shared storage
> > system.
>
> > andrew
>

> > 2010/10/7 Terry Camerlengo <terry.camerle...@gmail.com>

>
> > Why would you say FTP takes too much time? A typical export file compressed
> >> is around 7-8 GB per lane. On a network connection around 15 Mbs (the
> >> average rates at our institution) you are looking at a download time of 7-10
> >> minutes per lane.
>
> >> Not fast by any means, but considering the size of the files, it certainly
> >> beats burning things to DVDs and mailing it.
>

> >> 2010/10/7 Chulhong Kim <cybog...@gmail.com>

>
> >> Dear Siva
> >>> In our case we deliver the seq data to customer using Hdd. If you use the
> >>> FTP then it spend too much time.
> >>> Brst regards.
> >>> Chul Kim
>
> >>> 2010. 10. 7. 오후 11:04에 "Sivakumar Gowrisankar" <siv...@gmail.com>님이 작성:
>
> >>> Hi,
>
> >>> For those of you who are in a core lab, would you please share how you
> >>> deliver data to your customers? I am especially interested in the HiSeq
> >>> data.
>
> >>> Thank you
> >>> Siva
>
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