ok Brett :) No problem. I'll deal with you OICR guys just the same as anybody else on this list. If i feel it is relevant to the list I'll let you know if not, i'll just give them your email address. If you want to discuss it further I am happy to and I am sure we can find a solution to your liking but let's take this discussion offline now because people will start unsubscribing ;)
a On Thu, Nov 10, 2011 at 3:50 PM, Brett Whitty <[email protected]>wrote: > OK, maybe I misunderstood the initial question but it appeared to be > related to accessing ICGC BAM files from EGA; again, couldn't find the > original BioMart list post in my inbox to respond to it, and also didn't > feel my response (as OICR business) would be relevant to the BioMart user > community specifically. If you'd like to forward on requests from the list > I don't see a problem with it. No need to CC me though, just the support > email addresses. > > Brett > > From: Arek Kasprzyk <[email protected]> > Date: Wed, 9 Nov 2011 13:07:40 -0500 > To: Brett Whitty <[email protected]> > Cc: Claude Chelala <[email protected]>, Lincoln Stein < > [email protected]>, Francis Ouellette <[email protected]>, " > [email protected]" <[email protected]> > > Subject: Re: [BioMart Users] Query NGS data > > 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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