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huguesrichard / Allopipe

AlloPipe is a computational method to assess the alloreactivity expected from a donor/recipient transplantation pair
MIT License
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GRCh37 files parsing #19

Closed PierreLaville closed 2 months ago

PierreLaville commented 3 months ago
  1. Homo_sapiens.GRCh37.cdna.all.fa.gz downloaded from the Ensembl FTP
  2. Homo_sapiens.GRCh37.pep.all.fa.gz downloaded from the Ensembl FTP
  3. Homo_sapiens.GRCh37.refseq.tsv.gz downloaded from BioMart with default parameters (no filters) in early 2024:
    • Ensemble Genes 111

    • Human genes (GRCh37.p13)

      Modifications on the file:

    • "Transcript stable ID" column in headers renamed _"transcript_stableid" in order to fit with GRCh38 syntax
    • original name file: mart_export.txt renamed and compressed into Homo_sapiens.GRCh37.refseq.tsv.gz