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    • domingue's avatar
      Fixed issue related to missing gene names in more standard gtf annotations.... · 2315be90
      domingue authored
      Fixed issue related to missing gene names in more standard gtf annotations. Tested with Homo sapiens (Ensembl_v88_custom, GRCh38).
      2315be90
    • domingue's avatar
      Addresses issue #57. A GTF option has been included and now all gene... · 294dc4fd
      domingue authored
      Addresses issue #57. A GTF option has been included and now all gene information is extracted with the following hierarchy: GTF, gene_info table, biomaRT.
      It also uses the non-redundant exonic length (effective gene length) to calculate RPKMs and TPMs. If the GTF is not present it reverts to the old method.
      
      Tested with a planaria GTF, which does not contain gene names or any other information apart from ensembl_gene_id and transctipt_id. It might be good to test with a human / mouse GTF.
      
      TODO or at least to consider: (i) add GTF as a mandatory argument; (ii) use bioMart as a backup to find gene names and description if not present in the GTF (use case would some weird GTFs).
      294dc4fd
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