meetings
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
meetings [2008/02/12 13:41] – heidi | meetings [2008/10/20 15:42] (current) – heidi | ||
---|---|---|---|
Line 5: | Line 5: | ||
* [[21.01.2008]]: | * [[21.01.2008]]: | ||
* [[12.02.2008]]: | * [[12.02.2008]]: | ||
+ | * [[03.03.2008]]: | ||
+ | * [[14.03.2008]]: | ||
+ | * [[17.03.2008]]: | ||
+ | * ... | ||
+ | * [[06.06.2008]]: | ||
+ | * [[23.07.2008]]: | ||
+ | * [[20.10.2008]]: | ||
+ | |||
===== e-mails ===== | ===== e-mails ===== | ||
- | * 10.02.2008:< | + | |
- | Dear Howard, | + | * [[01.05.08]]: Laurent: phyloXML |
- | + | * [[21.05.08]]: Tinu: Converter von AFLPDat zu dem Selection Programm von Matthieu | |
- | Howard Cann wrote: | + | * [[09.06.08]]: Laurent: Blackwell Synergy - Mol Ecol Res, Volume 8 Issue 3 Page 578-580, May 2008 (Article Abstract) |
- | > 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 would be good to have, but I think there is no | + | |
- | 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 | + | |
- | </ | + | |
meetings.1202820062.txt.gz · Last modified: 2008/07/22 13:30 (external edit)