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Annotation of the genome - Hcv1a1d20200411
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@conchoecia conchoecia released this 12 Apr 17:40
· 35 commits to master since this release
Hcv1a1d20200411
1e0a453

The genome file is not included in this release .tar.gz. Download the genome file here: UCSC_Hcal_v1.fa.gz

This release contains annotation and protein files for the Hcalv1 genome. Most likely you will use files:

  • Hcv1a1d20200411_release/Hcv1a1d20200411_model_proteins.pep.gz
    • The model proteins for each transcript. NB - not all transcripts had CDS.
  • Hcv1a1d20200411_release/Hcv1a1d20200411_transcripts.fasta.gz
    • Transcript files generated directly from the genome. May contain prematurely truncated CDS.
  • Hcv1a1d20200411_release/Hcv1a1d20200411.gff.gz
    • Genome annotation of transcripts.
  • Hcv1a1d20200411_release/protein_size_table_Hcv1a1d20200411.csv
    • A table showing the protein size differences in the within-transcript-phased transcript haplotypes, as well as which was selected for the model proteins.
  • Hcv1a1d20200411_release/partly_phased/
    • Hcv1a1d20200411_release/partly_phased/h1_pilon_Hcv1a1d20200411.fasta.gz
      • Pseudohapltype h1 of within-transcript-phased transcripts. Each transcript is derived from a single haplotype, but it is not phased with respect to all other transcripts in the genome.
    • Hcv1a1d20200411_release/partly_phased/h1_Hcv1a1d20200411.pep.gz
      • Putative proteins from the above fasta file.
    • Hcv1a1d20200411_release/partly_phased/h2_pilon_Hcv1a1d20200411.fasta.gz
      • Pseudohaplotype h2 of the within-transcript-phased transcripts
    • Hcv1a1d20200411_release/partly_phased/h2_Hcv1a1d20200411.pep.gz
      • Putative proteins from the above fasta file.
  • Hcv1a1d20200411_release/phased/
    • Hcv1a1d20200411_release/phased/Hcv1a1d20200411_h1_phased_nucl.fasta.gz
      • Transcripts that are from h1. Matches the whole-genome phased vcf file.
    • Hcv1a1d20200411_release/phased/Hcv1a1d20200411_h1_phased_protein.pep.gz
      • Proteins from the above file.
    • Hcv1a1d20200411_release/phased/Hcv1a1d20200411_h2_phased_nucl.fasta.gz
      • Transcripts that are from h2. Matches the whole-genome phased vcf file.
    • Hcv1a1d20200411_release/phased/Hcv1a1d20200411_h2_phased_protein.pep.gz
      • Proteins from the above file.
    • Hcv1a1d20200411_release/phased/transcripts_unique_to_h1.Hcv1a1d20200411.list
      • Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file.
    • Hcv1a1d20200411_release/phased/transcripts_unique_to_h2.Hcv1a1d20200411.list
      • Same as above, but to h2. You probably won't need this file.
    • Hcv1a1d20200411_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1a1d20200411.list
      • Intermediate check that no transcripts are shared by both haplotypes. Should be empty.
    • Hcv1a1d20200411_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1a1d20200411.list
      • Final check that no transcripts are shared by both haplotypes. Should be empty.
Assets 3
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