Hi Brett, with the number of projects included in the BioMart mailing list (over 40) it is inpractical for the subscribers to remember support for every single one of them. As well, as mentioned previously questions and answers maybe of interest to a larger audience. We would therefore appreciate it if you took the trouble of cc'ing this list on your answers. I will personally ensure that anything related to the ICGC data is forwarded to you so you (unlike those supporting other BioMart projects) do not have to follow this mailing list.
cheers, a On Wed, Nov 9, 2011 at 12:46 PM, Brett Whitty <[email protected]>wrote: > Hi Arek et al., > > Sorry, with the volume of emails I receive from ICGC projects and others > I'm not actively following the BioMart list. > > I'd request anyone involved in the BioMart users lists with questions > related to the ICGC project or ICGC datasets to please send them to either > [email protected] or [email protected] respectively to ensure a prompt > response. > > Brett > > From: Arek Kasprzyk <[email protected]> > Date: Wed, 9 Nov 2011 06:02:11 -0500 > To: Claude Chelala <[email protected]> > Cc: Lincoln Stein <[email protected]>, Brett Whitty < > [email protected]>, Francis Ouellette <[email protected]>, " > [email protected]" <[email protected]> > Subject: Re: [BioMart Users] Query NGS data > > > Hi Claude, > I am glad that this is resolved :) and thank Brett and everyone else for > help. > > Brett: a small request for you. I try to make every possible effort to > make sure that the questions posted to this list get answered correctly and > in time. I occasionally forward the emails that are sent to me personally > to this list if I think they maybe of interest to others. It is a good > practice to reply to the questions that are posted there cc'ing the list as > well for two reasons: > > 1. It keeps me and others who monitor the replies to this list in the loop > 2. There are other subscribers who maybe interested in your reply > > > thank you > a > > On Wed, Nov 9, 2011 at 5:11 AM, Claude Chelala <[email protected]>wrote: > >> Dear All >> >> Many thanks for your replies and help. Brett kindly sent me the info on >> the access application. >> >> I have presented the breast cancer campaign tissue bank biomart portal at >> the NCRI conference yesterday and I am glad that the link we have through >> the ICGC data portal is as always the most popular among biologists! >> >> Regards >> Claude >> >> On 9 Nov 2011, at 03:11, "Arek Kasprzyk" <[email protected]> wrote: >> >> Hi Lincoln, >> I included him on my response to the list last week and i also sent him a >> reminder offline on monday but this is really not important because i am >> sure he was planning on replying anyway. I just wanted to speed things up >> for Claude and I am happy she is getting the help she needs. It does not >> matter who provides it. >> >> thank you >> a >> >> On Tue, Nov 8, 2011 at 10:01 PM, Lincoln Stein >> <[email protected]>wrote: >> >>> Hi Claude, >>> >>> I don't think Brett was actually Cc'd on the original response from >>> Arek. He will explain the details, but the most important thing to >>> understand is that you will need to apply for access to the controlled data >>> tier before you can download the raw WGS files. This is because genotyping >>> data can potentially be used to identify the donor, which is forbidden >>> under ICGC policies. >>> >>> Information on applying for controlled tier access is here: >>> http://www.icgc.org/daco >>> >>> Lincoln >>> >>> On Fri, Nov 4, 2011 at 2:43 PM, Arek Kasprzyk >>> <[email protected]>wrote: >>> >>>> Hi Claude, >>>> The ICGC WGS files are supposed to be deposited to EGA@EBI. I think >>>> the Spanish project is already deposited there. Perhaps some of the others >>>> too. If they are not there then they are most likely to be still with the >>>> centers that generated the data. The TCGA data included in the ICGC Portal >>>> is deposited elsewhere. I am cc'ing Brett Whitty who runs the ICGC Portal >>>> and liaises with all data providers. He will be able to give you more >>>> detailed information where everything is >>>> >>>> >>>> a >>>> >>>> >>>> >>>> >>>> >>>> On Fri, Nov 4, 2011 at 2:07 PM, Claude Chelala <[email protected]>wrote: >>>> >>>>> >>>>> If you can help us get one of the ICGC or sanger whole genome sequence >>>>> raw data file? >>>>> Claude >>>>> >>>>> >>>>> On 04/11/2011 18:04, "Arek Kasprzyk" <[email protected]> wrote: >>>>> >>>>> Hi Claude, >>>>> sorry, what projects are you talking about exactly? >>>>> >>>>> a >>>>> >>>>> >>>>> On Fri, Nov 4, 2011 at 2:00 PM, Claude Chelala <[email protected]> >>>>> wrote: >>>>> >>>>> Hi Arek >>>>> I was wondering if you could advise/help me to get a whole genome >>>>> sequence data file. There are none deposited in public repositories and >>>>> not >>>>> sure whom to ask. >>>>> Anonymous data is fine, we just need to test if our server can cope >>>>> with data analysis pipeline. >>>>> Thanks >>>>> Claude >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> This email may contain information that is privileged, confidential or >>>>> otherwise protected from disclosure. >>>>> It must not be used by, or its contents copied or disclosed to, >>>>> persons other than the addressee. >>>>> If you have received this email in error please notify the sender >>>>> immediately and delete the email. >>>>> This message has been scanned for viruses. >>>>> >>>>> >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Users mailing list >>>> [email protected] >>>> https://lists.biomart.org/mailman/listinfo/users >>>> >>>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Director, Informatics and Biocomputing Platform >>> Ontario Institute for Cancer Research >>> 101 College St., Suite 800 >>> Toronto, ON, Canada M5G0A3 >>> 416 673-8514 >>> Assistant: Renata Musa <[email protected]> >>> >> >> >
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