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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