Releases: conchoecia/hormiphora
Releases · conchoecia/hormiphora
Annotation of the genome - Hcv1.av93 - for zenodo
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:
Hcv1av93_release/Hcv1av93_model_proteins.pep.gz- The model proteins for each transcript. NB - not all transcripts had CDS.
Hcv1av93_release/Hcv1av93_transcripts.fasta.gz- Transcript files generated directly from the genome. May contain prematurely truncated CDS.
Hcv1av93_release/Hcv1av93.gff.gz- Genome annotation of transcripts.
Hcv1av93_release/protein_size_table_Hcv1av93.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.
Hcv1av93_release/partly_phased/Hcv1av93_release/partly_phased/h1_pilon_Hcv1av93.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.
Hcv1av93_release/partly_phased/h1_Hcv1av93.pep.gz- Putative proteins from the above fasta file.
Hcv1av93_release/partly_phased/h2_pilon_Hcv1av93.fasta.gz- Pseudohaplotype h2 of the within-transcript-phased transcripts
Hcv1av93_release/partly_phased/h2_Hcv1av93.pep.gz- Putative proteins from the above fasta file.
Hcv1av93_release/phased/Hcv1av93_release/phased/Hcv1av93_h1_phased_nucl.fasta.gz- Transcripts that are from h1. Matches the whole-genome phased vcf file.
Hcv1av93_release/phased/Hcv1av93_h1_phased_protein.pep.gz- Proteins from the above file.
Hcv1av93_release/phased/Hcv1av93_h2_phased_nucl.fasta.gz- Transcripts that are from h2. Matches the whole-genome phased vcf file.
Hcv1av93_release/phased/Hcv1av93_h2_phased_protein.pep.gz- Proteins from the above file.
Hcv1av93_release/phased/transcripts_unique_to_h1.Hcv1av93.list- Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file.
Hcv1av93_release/phased/transcripts_unique_to_h2.Hcv1av93.list- Same as above, but to h2. You probably won't need this file.
Hcv1av93_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1av93.list- Intermediate check that no transcripts are shared by both haplotypes. Should be empty.
Hcv1av93_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1av93.list- Final check that no transcripts are shared by both haplotypes. Should be empty.
Annotation of the genome - Hcv1.av93
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:
Hcv1av93_release/Hcv1av93_model_proteins.pep.gz- The model proteins for each transcript. NB - not all transcripts had CDS.
Hcv1av93_release/Hcv1av93_transcripts.fasta.gz- Transcript files generated directly from the genome. May contain prematurely truncated CDS.
Hcv1av93_release/Hcv1av93.gff.gz- Genome annotation of transcripts.
Hcv1av93_release/protein_size_table_Hcv1av93.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.
Hcv1av93_release/partly_phased/Hcv1av93_release/partly_phased/h1_pilon_Hcv1av93.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.
Hcv1av93_release/partly_phased/h1_Hcv1av93.pep.gz- Putative proteins from the above fasta file.
Hcv1av93_release/partly_phased/h2_pilon_Hcv1av93.fasta.gz- Pseudohaplotype h2 of the within-transcript-phased transcripts
Hcv1av93_release/partly_phased/h2_Hcv1av93.pep.gz- Putative proteins from the above fasta file.
Hcv1av93_release/phased/Hcv1av93_release/phased/Hcv1av93_h1_phased_nucl.fasta.gz- Transcripts that are from h1. Matches the whole-genome phased vcf file.
Hcv1av93_release/phased/Hcv1av93_h1_phased_protein.pep.gz- Proteins from the above file.
Hcv1av93_release/phased/Hcv1av93_h2_phased_nucl.fasta.gz- Transcripts that are from h2. Matches the whole-genome phased vcf file.
Hcv1av93_release/phased/Hcv1av93_h2_phased_protein.pep.gz- Proteins from the above file.
Hcv1av93_release/phased/transcripts_unique_to_h1.Hcv1av93.list- Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file.
Hcv1av93_release/phased/transcripts_unique_to_h2.Hcv1av93.list- Same as above, but to h2. You probably won't need this file.
Hcv1av93_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1av93.list- Intermediate check that no transcripts are shared by both haplotypes. Should be empty.
Hcv1av93_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1av93.list- Final check that no transcripts are shared by both haplotypes. Should be empty.
Annotation of the genome - Hcv1.av91
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:
Hcv1av91_release/Hcv1av91_model_proteins.pep.gz- The model proteins for each transcript. NB - not all transcripts had CDS.
Hcv1av91_release/Hcv1av91_transcripts.fasta.gz- Transcript files generated directly from the genome. May contain prematurely truncated CDS.
Hcv1av91_release/Hcv1av91.gff.gz- Genome annotation of transcripts.
Hcv1av91_release/protein_size_table_Hcv1av91.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.
Hcv1av91_release/partly_phased/Hcv1av91_release/partly_phased/h1_pilon_Hcv1av91.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.
Hcv1av91_release/partly_phased/h1_Hcv1av91.pep.gz- Putative proteins from the above fasta file.
Hcv1av91_release/partly_phased/h2_pilon_Hcv1av91.fasta.gz- Pseudohaplotype h2 of the within-transcript-phased transcripts
Hcv1av91_release/partly_phased/h2_Hcv1av91.pep.gz- Putative proteins from the above fasta file.
Hcv1av91_release/phased/Hcv1av91_release/phased/Hcv1av91_h1_phased_nucl.fasta.gz- Transcripts that are from h1. Matches the whole-genome phased vcf file.
Hcv1av91_release/phased/Hcv1av91_h1_phased_protein.pep.gz- Proteins from the above file.
Hcv1av91_release/phased/Hcv1av91_h2_phased_nucl.fasta.gz- Transcripts that are from h2. Matches the whole-genome phased vcf file.
Hcv1av91_release/phased/Hcv1av91_h2_phased_protein.pep.gz- Proteins from the above file.
Hcv1av91_release/phased/transcripts_unique_to_h1.Hcv1av91.list- Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file.
Hcv1av91_release/phased/transcripts_unique_to_h2.Hcv1av91.list- Same as above, but to h2. You probably won't need this file.
Hcv1av91_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1av91.list- Intermediate check that no transcripts are shared by both haplotypes. Should be empty.
Hcv1av91_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1av91.list- Final check that no transcripts are shared by both haplotypes. Should be empty.
Annotation of the genome - Hcv1.av87
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:
Hcv1av87_release/Hcv1av87_model_proteins.pep.gz- The model proteins for each transcript. NB - not all transcripts had CDS.
Hcv1av87_release/Hcv1av87_transcripts.fasta.gz- Transcript files generated directly from the genome. May contain prematurely truncated CDS.
Hcv1av87_release/Hcv1av87.gff.gz- Genome annotation of transcripts.
Hcv1av87_release/protein_size_table_Hcv1av87.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.
Hcv1av87_release/partly_phased/Hcv1av87_release/partly_phased/h1_pilon_Hcv1av87.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.
Hcv1av87_release/partly_phased/h1_Hcv1av87.pep.gz- Putative proteins from the above fasta file.
Hcv1av87_release/partly_phased/h2_pilon_Hcv1av87.fasta.gz- Pseudohaplotype h2 of the within-transcript-phased transcripts
Hcv1av87_release/partly_phased/h2_Hcv1av87.pep.gz- Putative proteins from the above fasta file.
Hcv1av87_release/phased/Hcv1av87_release/phased/Hcv1av87_h1_phased_nucl.fasta.gz- Transcripts that are from h1. Matches the whole-genome phased vcf file.
Hcv1av87_release/phased/Hcv1av87_h1_phased_protein.pep.gz- Proteins from the above file.
Hcv1av87_release/phased/Hcv1av87_h2_phased_nucl.fasta.gz- Transcripts that are from h2. Matches the whole-genome phased vcf file.
Hcv1av87_release/phased/Hcv1av87_h2_phased_protein.pep.gz- Proteins from the above file.
Hcv1av87_release/phased/transcripts_unique_to_h1.Hcv1av87.list- Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file.
Hcv1av87_release/phased/transcripts_unique_to_h2.Hcv1av87.list- Same as above, but to h2. You probably won't need this file.
Hcv1av87_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1av87.list- Intermediate check that no transcripts are shared by both haplotypes. Should be empty.
Hcv1av87_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1av87.list- Final check that no transcripts are shared by both haplotypes. Should be empty.
Annotation of the genome - Hcv1.av86
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:
Hcv1av86_release/Hcv1av86_model_proteins.pep.gz- The model proteins for each transcript. NB - not all transcripts had CDS.
Hcv1av86_release/Hcv1av86_transcripts.fasta.gz- Transcript files generated directly from the genome. May contain prematurely truncated CDS.
Hcv1av86_release/Hcv1av86.gff.gz- Genome annotation of transcripts.
Hcv1av86_release/protein_size_table_Hcv1av86.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.
Hcv1av86_release/partly_phased/Hcv1av86_release/partly_phased/h1_pilon_Hcv1av86.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.
Hcv1av86_release/partly_phased/h1_Hcv1av86.pep.gz- Putative proteins from the above fasta file.
Hcv1av86_release/partly_phased/h2_pilon_Hcv1av86.fasta.gz- Pseudohaplotype h2 of the within-transcript-phased transcripts
Hcv1av86_release/partly_phased/h2_Hcv1av86.pep.gz- Putative proteins from the above fasta file.
Hcv1av86_release/phased/Hcv1av86_release/phased/Hcv1av86_h1_phased_nucl.fasta.gz- Transcripts that are from h1. Matches the whole-genome phased vcf file.
Hcv1av86_release/phased/Hcv1av86_h1_phased_protein.pep.gz- Proteins from the above file.
Hcv1av86_release/phased/Hcv1av86_h2_phased_nucl.fasta.gz- Transcripts that are from h2. Matches the whole-genome phased vcf file.
Hcv1av86_release/phased/Hcv1av86_h2_phased_protein.pep.gz- Proteins from the above file.
Hcv1av86_release/phased/transcripts_unique_to_h1.Hcv1av86.list- Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file.
Hcv1av86_release/phased/transcripts_unique_to_h2.Hcv1av86.list- Same as above, but to h2. You probably won't need this file.
Hcv1av86_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1av86.list- Intermediate check that no transcripts are shared by both haplotypes. Should be empty.
Hcv1av86_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1av86.list- Final check that no transcripts are shared by both haplotypes. Should be empty.
Annotation of the genome - Hcv1.av85
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:
Hcv1av85_release/Hcv1av85_model_proteins.pep.gz- The model proteins for each transcript. NB - not all transcripts had CDS.
Hcv1av85_release/Hcv1av85_transcripts.fasta.gz- Transcript files generated directly from the genome. May contain prematurely truncated CDS.
Hcv1av85_release/Hcv1av85.gff.gz- Genome annotation of transcripts.
Hcv1av85_release/protein_size_table_Hcv1av85.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.
Hcv1av85_release/partly_phased/Hcv1av85_release/partly_phased/h1_pilon_Hcv1av85.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.
Hcv1av85_release/partly_phased/h1_Hcv1av85.pep.gz- Putative proteins from the above fasta file.
Hcv1av85_release/partly_phased/h2_pilon_Hcv1av85.fasta.gz- Pseudohaplotype h2 of the within-transcript-phased transcripts
Hcv1av85_release/partly_phased/h2_Hcv1av85.pep.gz- Putative proteins from the above fasta file.
Hcv1av85_release/phased/Hcv1av85_release/phased/Hcv1av85_h1_phased_nucl.fasta.gz- Transcripts that are from h1. Matches the whole-genome phased vcf file.
Hcv1av85_release/phased/Hcv1av85_h1_phased_protein.pep.gz- Proteins from the above file.
Hcv1av85_release/phased/Hcv1av85_h2_phased_nucl.fasta.gz- Transcripts that are from h2. Matches the whole-genome phased vcf file.
Hcv1av85_release/phased/Hcv1av85_h2_phased_protein.pep.gz- Proteins from the above file.
Hcv1av85_release/phased/transcripts_unique_to_h1.Hcv1av85.list- Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file.
Hcv1av85_release/phased/transcripts_unique_to_h2.Hcv1av85.list- Same as above, but to h2. You probably won't need this file.
Hcv1av85_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1av85.list- Intermediate check that no transcripts are shared by both haplotypes. Should be empty.
Hcv1av85_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1av85.list- Final check that no transcripts are shared by both haplotypes. Should be empty.
Annotation of the genome - Hcv1.av84
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:
Hcv1av84_release/Hcv1av84_model_proteins.pep.gz- The model proteins for each transcript. NB - not all transcripts had CDS.
Hcv1av84_release/Hcv1av84_transcripts.fasta.gz- Transcript files generated directly from the genome. May contain prematurely truncated CDS.
Hcv1av84_release/Hcv1av84.gff.gz- Genome annotation of transcripts.
Hcv1av84_release/protein_size_table_Hcv1av84.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.
Hcv1av84_release/partly_phased/Hcv1av84_release/partly_phased/h1_pilon_Hcv1av84.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.
Hcv1av84_release/partly_phased/h1_Hcv1av84.pep.gz- Putative proteins from the above fasta file.
Hcv1av84_release/partly_phased/h2_pilon_Hcv1av84.fasta.gz- Pseudohaplotype h2 of the within-transcript-phased transcripts
Hcv1av84_release/partly_phased/h2_Hcv1av84.pep.gz- Putative proteins from the above fasta file.
Hcv1av84_release/phased/Hcv1av84_release/phased/Hcv1av84_h1_phased_nucl.fasta.gz- Transcripts that are from h1. Matches the whole-genome phased vcf file.
Hcv1av84_release/phased/Hcv1av84_h1_phased_protein.pep.gz- Proteins from the above file.
Hcv1av84_release/phased/Hcv1av84_h2_phased_nucl.fasta.gz- Transcripts that are from h2. Matches the whole-genome phased vcf file.
Hcv1av84_release/phased/Hcv1av84_h2_phased_protein.pep.gz- Proteins from the above file.
Hcv1av84_release/phased/transcripts_unique_to_h1.Hcv1av84.list- Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file.
Hcv1av84_release/phased/transcripts_unique_to_h2.Hcv1av84.list- Same as above, but to h2. You probably won't need this file.
Hcv1av84_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1av84.list- Intermediate check that no transcripts are shared by both haplotypes. Should be empty.
Hcv1av84_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1av84.list- Final check that no transcripts are shared by both haplotypes. Should be empty.
Annotation of the genome - Hcv1a1d20200426
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:
Hcv1a1d20200426_release/Hcv1a1d20200426_model_proteins.pep.gz- The model proteins for each transcript. NB - not all transcripts had CDS.
Hcv1a1d20200426_release/Hcv1a1d20200426_transcripts.fasta.gz- Transcript files generated directly from the genome. May contain prematurely truncated CDS.
Hcv1a1d20200426_release/Hcv1a1d20200426.gff.gz- Genome annotation of transcripts.
Hcv1a1d20200426_release/protein_size_table_Hcv1a1d20200426.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.
Hcv1a1d20200426_release/partly_phased/Hcv1a1d20200426_release/partly_phased/h1_pilon_Hcv1a1d20200426.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.
Hcv1a1d20200426_release/partly_phased/h1_Hcv1a1d20200426.pep.gz- Putative proteins from the above fasta file.
Hcv1a1d20200426_release/partly_phased/h2_pilon_Hcv1a1d20200426.fasta.gz- Pseudohaplotype h2 of the within-transcript-phased transcripts
Hcv1a1d20200426_release/partly_phased/h2_Hcv1a1d20200426.pep.gz- Putative proteins from the above fasta file.
Hcv1a1d20200426_release/phased/Hcv1a1d20200426_release/phased/Hcv1a1d20200426_h1_phased_nucl.fasta.gz- Transcripts that are from h1. Matches the whole-genome phased vcf file.
Hcv1a1d20200426_release/phased/Hcv1a1d20200426_h1_phased_protein.pep.gz- Proteins from the above file.
Hcv1a1d20200426_release/phased/Hcv1a1d20200426_h2_phased_nucl.fasta.gz- Transcripts that are from h2. Matches the whole-genome phased vcf file.
Hcv1a1d20200426_release/phased/Hcv1a1d20200426_h2_phased_protein.pep.gz- Proteins from the above file.
Hcv1a1d20200426_release/phased/transcripts_unique_to_h1.Hcv1a1d20200426.list- Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file.
Hcv1a1d20200426_release/phased/transcripts_unique_to_h2.Hcv1a1d20200426.list- Same as above, but to h2. You probably won't need this file.
Hcv1a1d20200426_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1a1d20200426.list- Intermediate check that no transcripts are shared by both haplotypes. Should be empty.
Hcv1a1d20200426_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1a1d20200426.list- Final check that no transcripts are shared by both haplotypes. Should be empty.
Annotation of the genome - Hcv1a1d20200414
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:
Hcv1a1d20200414_release/Hcv1a1d20200414_model_proteins.pep.gz- The model proteins for each transcript. NB - not all transcripts had CDS.
Hcv1a1d20200414_release/Hcv1a1d20200414_transcripts.fasta.gz- Transcript files generated directly from the genome. May contain prematurely truncated CDS.
Hcv1a1d20200414_release/Hcv1a1d20200414.gff.gz- Genome annotation of transcripts.
Hcv1a1d20200414_release/protein_size_table_Hcv1a1d20200414.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.
Hcv1a1d20200414_release/partly_phased/Hcv1a1d20200414_release/partly_phased/h1_pilon_Hcv1a1d20200414.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.
Hcv1a1d20200414_release/partly_phased/h1_Hcv1a1d20200414.pep.gz- Putative proteins from the above fasta file.
Hcv1a1d20200414_release/partly_phased/h2_pilon_Hcv1a1d20200414.fasta.gz- Pseudohaplotype h2 of the within-transcript-phased transcripts
Hcv1a1d20200414_release/partly_phased/h2_Hcv1a1d20200414.pep.gz- Putative proteins from the above fasta file.
Hcv1a1d20200414_release/phased/Hcv1a1d20200414_release/phased/Hcv1a1d20200414_h1_phased_nucl.fasta.gz- Transcripts that are from h1. Matches the whole-genome phased vcf file.
Hcv1a1d20200414_release/phased/Hcv1a1d20200414_h1_phased_protein.pep.gz- Proteins from the above file.
Hcv1a1d20200414_release/phased/Hcv1a1d20200414_h2_phased_nucl.fasta.gz- Transcripts that are from h2. Matches the whole-genome phased vcf file.
Hcv1a1d20200414_release/phased/Hcv1a1d20200414_h2_phased_protein.pep.gz- Proteins from the above file.
Hcv1a1d20200414_release/phased/transcripts_unique_to_h1.Hcv1a1d20200414.list- Transcripts that were able to be assigned to haplotype 1 (h1) of the whole-genome phasing. You probably won't need this file.
Hcv1a1d20200414_release/phased/transcripts_unique_to_h2.Hcv1a1d20200414.list- Same as above, but to h2. You probably won't need this file.
Hcv1a1d20200414_release/phased/transcripts_shared_by_both_should_be_empty.Hcv1a1d20200414.list- Intermediate check that no transcripts are shared by both haplotypes. Should be empty.
Hcv1a1d20200414_release/phased/second_list_of_transcripts_shared_by_both_should_be_empty.Hcv1a1d20200414.list- Final check that no transcripts are shared by both haplotypes. Should be empty.
Annotation of the genome - Hcv1a1d20200411
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.