File release

Data structure

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 LATEST_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 sometimes 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

• https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_009 - recommended version for the Feb meeting
• https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_008
• https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_007
• https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_006
• https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_005
• https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_004
• https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_003
• https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_002
• https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_001