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MtDNA help needed please!!!

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  • #16
    Hi Cacio,
    Thanks for that, I'm just trying to open the thing and not succeeding!!! Word is just a load of weird symbols as is notepad...excel leaves bits out....

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    • #17
      Strange. I just re-tried here. I download a *.zip file. Then I unzip it. I get three files, one of which is deCODEme_scan.csv . I can open this without problems in notepad. (I have the newer version of excel, and it opens there too, after a while, though I suspect this won't work in earlier versions).
      did you unzip the files first?

      cacio

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      • #18
        Nope, just complete random symbols with the odd DeCode mentioned every now and then. Have tried opening in word, wordpad, notepad, excel
        Maybe 2003 is too old? Excel works but only for the first 65,000 rows.
        It told me to work in word, shrink the info into smaller files then convert them to excel files, but I can't get it to open in word!!!
        You know when you say unzip the files, do you mean open the big file that then reveals 3 documents?

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        • #19
          Yes, I mean the program that extracts 3 files from the original file .zip that is downloaded. It should generate 3 files, one of which is deCODEme_scan.csv

          deCODEme_scan.csv file should be a plain text file in comma delimited forms. One should be able to open deCODEme_scan.csv with any text editor, for instance, Wordpad.

          cacio

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          • #20
            Hi Cacio,
            How are you opening the file as a text rich format? Are you saving the file first? My browser asks me if I want to open it or save it. If I save it and unzip the file, it appears as an excel document which I can't change.
            If I open it using word, wordpad or notepad, it's not readable.

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            • #21
              That's what I do: download the file from the website and save it to a directory. The file is called something like cacio.zip. It's a zip file and thus not readable.

              If I doubleclick on this cacio.zip file, the program Winzip opens (ie the program to unzip files). Whether this is the case, depends on whether one has the program installed and whether it is linked.

              Using Winzip, I then extract the files. I obtain three files, as said previously, one of which is called deCODEME_scan.csv. Note: you need to *extract* them, that is, three files should appear in the relevant directory and remain there when you close the program to unzip them. I close winzip and then move to notepad.

              The deCODEme_scan.csv file should be a comma separated file, that is, a text file. Often, they are associated with excel, so if one doubleclicks on deCODEme_scan.csv, excel opens. However, one should be able to open wordpad or the like, and then manually open this file.

              cacio

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              • #22
                [QUOTE=cacio;149023]Burto:


                The line I was talking about is the following:
                MitoT14767C,C/T,M,14766,+,TT

                Got it!!! Can't find this one though?! The closest I can find is T14799C

                Another indicative line is
                MitoG2708A,A/G,M,2706,+,GG

                G indicates "outside H", A indicates H.

                That one says AA

                What does that mean? Thanks for your help!
                Last edited by burto; 2 April 2009, 10:44 AM.

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                • #23
                  My God that is so complicated! I don't have winzip, word, or excel or any of that. I didn't know that just to read it was so complicated. A pdf would be better, that is what DNA Tribes uses. I thought that was difficult because I didn't have Adobe Reader. AncestryByDna sent my info on a dvd, and I purchased the book form (when I expected the Euro.1).

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                  • #24
                    Burto:

                    2706 A means that you are in H. You can check the following graph:

                    http://mbe.oxfordjournals.org/conten...209f02_lw.jpeg

                    as you can see, 2706A is at the root of H.

                    Strange that they don't have 14766... I have the following ones around it:
                    MitoA14234G,A/G,M,14233,+,AA
                    MitoA14583G,A/G,M,14582,+,AA
                    MitoT14767C,C/T,M,14766,+,TT
                    MitoT14784C,C/T,M,14783,+,TT
                    MitoT14799C,C/T,M,14798,+,TT

                    14766 is usually how they assign HV. Perhaps that's the reason they only assigned you to the "mother" haplogroup. However, 2706 should be indicative.

                    I don't know which positions are checked by decodeme, but now that you have it open, you can peruse the graph above and your data to see if you find anything else.

                    cacio

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                    • #25
                      Hi,
                      Thanks for that. They have told me I'm on the borders of H and R* so maybe it is just picking up the older bits to H or like you say, if 14766 is missing then this may be why. I'll ask them another time. Can any of the numbers on that graph be compared to mine to see if I match a sub group? That 2706 I mentioned says AA does that count as 1 A on that graph so if the graph says C I need CC?

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                      • #26
                        Its simple...

                        Burto,

                        Its very simply...Your a human bean!
                        O.K. joking a side, thats confusing!

                        Maria

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                        • #27
                          Hmm...I think I get it...so the numbers on that graph, let's say 3992T# on the H4a branch, I look on my info and find this: MitoC3993T,C/T,M,3992,
                          is that right? I match the numbers in bold? And if so, then to be part of H4a I would need TT rather than CC?

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                          • #28
                            Good luck...

                            Burto,
                            Sorry I can't help you. I understand autosomal markers much better but I wish you the very best...I will leave mtDNA to the experts...

                            Maria

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                            • #29
                              Thank you! Think I've got it but would like advice first!!

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                              • #30
                                Burto:

                                yes, that is the way to read the numbers. You have to look at the position in the mtdna (the number you have in bold) and check which value you have. In general, if you match the value in the tree, you should be in that branch. I am not an expert on H, so I don't know which snps are more important, but that's the way to read them. That's why i said 2706 puts you into H.

                                Since decodeme only tests a few position, there's so much you can do, but it is of course possible that you happen to have one of the values. The most common subgroup of H is H1, so check what you have at 3010, ie
                                MitoG3012A,A/G,M,3010,+,GG
                                AA instead corresponds to H1.

                                There is only one letter at each location, A,C,G, or T. Decodeme writes two (AA,CC, etc.) in the file, but it's really only one.

                                cacio

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