File release

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Data overview

All the data produced in the FANTOM5 collaboration will be shared by any of the FANTOM5 collaborators to encourage a wide range of analysis with following the FANTOM5 rules. Please note that all the data is confidential and don't share with other people before public release. The update of the data (mainly addition of transcriptome profiles) is going to happen routinely. At some stages, in accordance with the status of the main paper analysis/project phases, we are going to make several data freeze, which is a unit of data submission/publication to public. Please read FANTOM5_overview for the project plan.

Shared directory is for the preliminary analyses. The primary data is in LATEST_UPDATE, which is produced by the FANTOM5 production group (WP2). Contributed analysis performed separately from the production pipeline and external relevant data set to be shared commonly are also maintained here. We will make data freeze for paper writing, when needed (not available yet)

This page is about UPDATE.

Known issue

Issues that will be corrected in the next release

  • strange symbols in the sample name: CNhs11316
  • inconsistent sample name (t cell / T cell)
  • three libraries are in wrong categories (tissue / primary cells)

Issues that will be corrected at some stage

  • Incomplete 'study' SDRF : process after sequencing
    • file names will be added at some stage
    • sex (male/female/unknown) information used in the mapping will be added at some stage.
  • Genomic coordinates of HeliScopeCAGE reads rarely strange (beyond chromosomal size)
    • BAM file (delve mapping file) and CTSS files will be updated at some stage. Note that It only affects tens of reads.
  • Long reads (>64bp) of HeliScoeCAGE are mapped wrongly. Note that most of such long reads are bad reads (CTAG repeats, a.k.a BAO)
  • '@PG' tags in the BAM files is not included for some libraries

Updates

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