meetings
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meetings [2008/06/10 09:04] – heidi | meetings [2008/10/20 15:42] (current) – heidi | ||
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* [[06.06.2008]]: | * [[06.06.2008]]: | ||
+ | * [[23.07.2008]]: | ||
+ | * [[20.10.2008]]: | ||
===== e-mails ===== | ===== e-mails ===== | ||
- | + | * [[10.02.08]]: Laurent: file format (Howard Cann) | |
- | ==== 10.02.2008 ==== | + | * [[01.05.08]]: Laurent: phyloXML |
- | Dear Howard,\\ | + | * [[21.05.08]]: Tinu: Converter von AFLPDat zu dem Selection Programm von Matthieu |
- | + | * [[09.06.08]]: Laurent: Blackwell Synergy | |
- | Howard Cann wrote: | + | |
- | > Dear Laurent, | + | |
- | > | + | |
- | > Until now, the HGDP-CEPH diversity panel database has stored and | + | |
- | > displayed marker genotypes generated on the panel population samples. | + | |
- | > It is time that we receive sequences from panel users who are | + | |
- | > resequencing in the panel in order to study human variation, estimate | + | |
- | > diversity indices, describe human demography/ | + | |
- | + | ||
- | Sounds good! | + | |
- | + | ||
- | > What file formats should we be ready to receive? | + | |
- | + | ||
- | Some flat file format | + | |
- | general agreement on how these large resequencing files should be | + | |
- | formatted. I have a MSc student with whom we are beginning to think | + | |
- | about such a format. We are investigating the possibility to have some | + | |
- | xml coded file, that would be efficient for resequencing data, but we | + | |
- | are still in the first development phase. | + | |
- | > How should we suggest to contributors to code their sequence data (nt | + | |
- | > letters or numbers), to code missing bases.......? | + | |
- | I guess it would be most useful if sequences would be grouped by | + | |
- | population, with info on:\\ | + | |
- | + | ||
- | Sequence region (chromosomic region) | + | |
- | Sequence begin | + | |
- | Sequence length | + | |
- | Population where it was sequenced | + | |
- | Individual in which it was sequenced | + | |
- | Geographic coordinate of the population or of the individual | + | |
- | Linguistic group or language family of the individual or population | + | |
- | Tag indicating is sequence phase has been inferred, with pointer to the | + | |
- | other complementary sequence | + | |
- | Nucleotide should be coded as ACGT, and ? for missing data (which makes | + | |
- | intuitive sense), otherwise common letters for ambiguous nucleotide | + | |
- | assignment | + | |
- | + | ||
- | > What other questions should I be asking you in order to set up a | + | |
- | > sequence db that will be useful to scientists in the field of human | + | |
- | > population genetics. | + | |
- | + | ||
- | Some information on whether it is coding sequence or not, with the start | + | |
- | of the coding region, would be nice to have. Some link to some other | + | |
- | data base (e.g. ensembl) where additional information can be found would | + | |
- | be nice as well. | + | |
- | + | ||
- | > I think that CEPH should be concerned with managing and maintaining | + | |
- | > the sequences in the db and not with computing various parmeters of | + | |
- | > polymorphism, | + | |
- | > are capable of doing. | + | |
- | + | ||
- | Yes, you are right, but some summary statistics could be useful to | + | |
- | compute.\\ | + | |
- | + | ||
- | It would also be nice to be able to extract, say all sequences or | + | |
- | polymorphism in a given chromosomal region.\\ | + | |
- | + | ||
- | Cheers | + | |
- | laurent | + | |
- | + | ||
- | + | ||
- | ==== 09.06.2008 ==== | + | |
- | Hi Heidi,\\ | + | |
- | + | ||
- | please have a look at the following paper and program... | + | |
- | + | ||
- | [[http:// | + | |
- | + | ||
- | It would be worth looking at...\\ | + | |
- | + | ||
- | cheers | + | |
- | laurent | + | |
- | + | ||
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