meetings
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- | * [[21.05.08]]: | + | * [[21.05.08]]: Tinu: Converter von AFLPDat zu dem Selection Programm von Matthieu |
* [[09.06.08]]: | * [[09.06.08]]: | ||
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- | ==== 10.02.2008 ==== | ||
- | Dear Howard,\\ | ||
- | |||
- | 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 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 | ||
- | |||
- | |||
- | ==== 09.06.2008 ==== | ||
- | Hi Heidi,\\ | ||
- | |||
- | please have a look at the following paper and program... | ||
- | |||
- | [[http:// | ||
- | |||
- | It would be worth looking at...\\ | ||
- | |||
- | cheers | ||
- | laurent | ||
- | |||
- | |||
meetings.1213082089.txt.gz · Last modified: 2008/07/22 13:30 (external edit)