Changes between Version 9 and Version 10 of PombasePlanningMeetingAgenda20141017


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Timestamp:
Oct 17, 2014, 11:54:41 AM (6 years ago)
Author:
al637
Comment:

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  • PombasePlanningMeetingAgenda20141017

    v9 v10  
    6161== Display of new data types ==
    6262Phenotyping of wild strains, how to display these?
     63
     64From Dan:
     65 Here is what  think might be interesting/useful to represent.
     66
     67The three main ones are:
     68
     691. SNPs, indels using Ensembles variation tools. I think I jhave already sent a VCF for indels and SNPs. If not I'm happy to send this again.
     702. Tf1 transposons that are variable between strains as well. Could also be supplied in VCF.
     713. Variation wiggle tracks (like pi, which is the average pairwise differences, for example).
     72
     73Also:
     74Some of the variants are associated with one or more traits (they are QTLS). I think QTLs are displayed on some other species. This would be a small amount of data, perhaps 100 or so QTLs.
     75I am not sure how much of this data gets displayed in gene pages. If its des then fine. Otherwise I could easily make a table of gene-by-gene stats (such as number of Snps, indels, pi, and andy QTLs).
     76
     77I'd be very happy to come along & help/chat about getting this data into pombase.
     78
    6379
    6480 == Priority Jira tickets ==