Changes between Version 46 and Version 47 of InhouseMeetingQuestions


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Timestamp:
Dec 9, 2011, 2:46:51 PM (10 years ago)
Author:
antonialock
Comment:

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  • InhouseMeetingQuestions

    v46 v47  
    1212
    1313'''Feedback from retreat''' [[BR]]
    14 •       Genome visualization in Ensembl. A feature that allows scrolling left and right like in X-map would be useful
    15 •       RNA-seq data (and chip-seq). Does Ensembl support squiggly data tracks or only boxes? Comparison between species would be useful, showing conserved refions, like in UCSC.
    16 o       Intra-species variation and SNP’s – wiggle tracks for gene diversity
    17 •       Multiple data-sets on tracks. Make them searchable. Show one as consensus and the others beneath. Data-sets should be searchable and suppressible.
    18 •       Will our data be loaded into Biogrid? Many people who do not use PomBase may use Biogrid.
    19 •       Could make a Pombe wiki where academics can freetype pombe facts. Different pages for different features/conditions or whatever. Suppress text from people who talk rubbish.
    20 •       E-QTL data – show in the genome browser and on gene-pages. Human ensemble may already do this. Might be difficult to do on tracks.
    21 •       Protein modifications – show on the protein sequence. Also map out functional regions, catalytic residues.
    22 •       All data should be downloadable.
    23 •       Support a repository for alignmemts. Dan had problems with a publication once because there was nowhere where he could publically store his alignment.
    24 o       Genome scale alignments
    25 •       Transcript boxes: this needs to be referenced and show what data-sets that have been used to define UTR’s etc.
    26 o       Evidence codes could also be shown.
    27 o       If multiple alternatives the data could be shown on tracks.
    28 o       There should be links to papers.
    29 o       They could be searchable and suppressible.
    30 o       RNA seq data
    31 o       Different transcripts under different conditions could be shown
     14•       Genome visualization in Ensembl. A feature that allows scrolling left and right like in X-map would be useful [[BR]]
     15•       RNA-seq data (and chip-seq). Does Ensembl support squiggly data tracks or only boxes? Comparison between species would be useful, showing conserved refions, like in UCSC. [[BR]]
     16o       Intra-species variation and SNP’s – wiggle tracks for gene diversity [[BR]]
     17•       Multiple data-sets on tracks. Make them searchable. Show one as consensus and the others beneath. Data-sets should be searchable and suppressible. [[BR]]
     18•       Will our data be loaded into Biogrid? Many people who do not use PomBase may use Biogrid. [[BR]]
     19•       Could make a Pombe wiki where academics can freetype pombe facts. Different pages for different features/conditions or whatever. Suppress text from people who talk rubbish. [[BR]]
     20•       E-QTL data – show in the genome browser and on gene-pages. Human ensemble may already do this. Might be difficult to do on tracks. [[BR]]
     21•       Protein modifications – show on the protein sequence. Also map out functional regions, catalytic residues.[[BR]]
     22•       All data should be downloadable. [[BR]]
     23•       Support a repository for alignmemts. Dan had problems with a publication once because there was nowhere where he could publically store his alignment. [[BR]]
     24        o Genome scale alignments [[BR]]
     25•       Transcript boxes: this needs to be referenced and show what data-sets that have been used to define UTR’s etc. [[BR]]
     26        o Evidence codes could also be shown. [[BR]]
     27        o If multiple alternatives the data could be shown on tracks. [[BR]]
     28        o There should be links to papers. [[BR]]
     29        o They could be searchable and suppressible. [[BR]]
     30        o RNA seq data [[BR]]
     31        o Different transcripts under different conditions could be shown [[BR]]
    3232
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