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337 Data files visible to you, out of a total of 353

/output/alt.cds.IDs

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_03_components_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_03_components_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:55, Last updated: 12th Apr 2020 at 09:30

/output/alt.aa.IDs

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_03_components_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_03_components_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:55, Last updated: 12th Apr 2020 at 09:30

/scripts/commands-components_1_3cvs-gffmerged.txt

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_03_components_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_03_components_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:56, Last updated: 12th Apr 2020 at 09:28

/reports/SupplementaryFigure4.pdf

_p_stRT

Supplementary Figure 3 - Venn diagrams showing the overlap of paralogue clusters in cultivar-specific transcriptomes and merged Phureja DM gene model. Representatives and alternatives of the stPanTr (pan-transcriptome) paralogue cluster are counted as well as alternatives defined at stCuSTr (cultivar-specific transcriptome) step. For Phureja, the merged ITAG and PGSC DM gene models were counted. Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged/reports/

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3409.2

Investigations: _I_STRT

Studies: SupplementaryInformation, _S_04_stPanTr

Assays: Supplementary Information, _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:01, Last updated: 11th Apr 2020 at 23:22

/reports/SupplementaryTableS7

_p_stRT

Supplementary Table S7 - Paralogue cluster information for cultivar-specific and pantranscriptome sequences extended with annotations and quality classification. Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged/reports/

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3721.2

Investigations: _I_STRT

Studies: SupplementaryInformation, _S_04_stPanTr

Assays: Supplementary Information, _A_02_cdhit_3cvs-GFFmerged

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Created: 8th Apr 2020 at 16:27, Last updated: 11th Apr 2020 at 23:22

/output/VennDiagrams/stPanTr+stCuSTr_geneCount_weak-components.tiff

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:53, Last updated: 11th Apr 2020 at 22:32

/output/VennDiagrams/stPanTr_geneCount_weak-components_repOnly.tiff

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:53, Last updated: 11th Apr 2020 at 22:32

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep+alt_perc.tiff

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:53, Last updated: 11th Apr 2020 at 22:31

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep+alt_and_stCuSTr_alt_perc.tiff

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:53, Last updated: 11th Apr 2020 at 22:30

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep+alt_and_stCuSTr_alt.tiff

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:53, Last updated: 11th Apr 2020 at 22:30

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep+alt.tiff

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:53, Last updated: 11th Apr 2020 at 22:29

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep_perc.tiff

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:52, Last updated: 11th Apr 2020 at 22:29

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep.tiff

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:52, Last updated: 11th Apr 2020 at 22:28

/output/VennDiagrams/stPanTr_geneCount_weak-components.tiff

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:52, Last updated: 11th Apr 2020 at 22:27

/output/stPanTr-clusters.tsv

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:51, Last updated: 11th Apr 2020 at 22:24

/output/cdhit-est_singletons_aS.75_c.90.tsv

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:50, Last updated: 11th Apr 2020 at 22:23

/output/cdhit-est_representativesMatched_aS.75_c.90.tsv

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:50, Last updated: 11th Apr 2020 at 22:23

/output/cdhit-est_rep-alt_aS.75_c.90_pairs.tsv

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:50, Last updated: 11th Apr 2020 at 22:22

/output/annot.alias.cds.tsv

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:50, Last updated: 11th Apr 2020 at 22:20

/output/annot.alias.aa.tsv

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:50, Last updated: 11th Apr 2020 at 22:19

/output/5cv_weak-components_withAnnotation.tsv

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:50, Last updated: 11th Apr 2020 at 22:18

/output/5cv_weak-components.txt

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:50, Last updated: 11th Apr 2020 at 22:15

/scripts/04_summary_stPanTr_v4.html

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

Download

Created: 19th Mar 2020 at 10:54, Last updated: 11th Apr 2020 at 22:05

/scripts/03_stPanTr_components_all.html

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:54, Last updated: 11th Apr 2020 at 22:03

/scripts/02_cd-hit-est_cdhit-2d.html

_p_stRT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 19th Mar 2020 at 10:54, Last updated: 11th Apr 2020 at 22:02

/reports/SupplementaryTableS1

_p_stRT

Supplementary Table S1 - Detailed sample information table used to generate the de novo transcriptome assemblies. Raw and processed reads summary. Layer _p_stRT/_I_STRT/ _S_01_sequences/reports

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3090.1

Investigations: _I_STRT

Studies: SupplementaryInformation

Assays: Supplementary Information

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Created: 6th Nov 2019 at 14:25, Last updated: 8th Apr 2020 at 16:39

/reports/SupplementaryTableS2

_p_stRT

Supplementary Table S2 - Detailed de novo assemblies information table. Primary potato transcriptome assemblies summary listing parameters used for short-read de novo assembly generation. Layer _p_stRT/_I_STRT/_S_02_denovo/reports/

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3091.1

Investigations: _I_STRT

Studies: SupplementaryInformation

Assays: Supplementary Information

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Created: 6th Nov 2019 at 14:40, Last updated: 8th Apr 2020 at 16:39

/reports/SupplementaryFigure1.pdf

_p_stRT

Number of transcripts from de novo assemblies contributing to cultivar Désirée, transcriptome and number of complete BUSCOs found in assemblies. Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet.

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3107.1

Investigations: _I_STRT

Studies: SupplementaryInformation, _S_03_stCuSTr

Assays: Supplementary Information, _A_02.2_assembly-contribution-count

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Created: 15th Nov 2019 at 17:57, Last updated: 8th Apr 2020 at 16:37

SupplementaryFile1

_p_stRT

Supplementary File 1 - Merged ITAG/PGSC Phureja DM gene models. Archive containing GTF, CDS and peptide fasta files for merged ITAG and PGSC gene models for S. tuberosum Group Phureja DM genome v4.04

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3408.1

Investigations: _I_STRT

Studies: SupplementaryInformation

Assays: Supplementary Information

Download

Created: 19th Mar 2020 at 09:57, Last updated: 7th Apr 2020 at 13:53

/reports/SupplementaryTableS6

_p_stRT

Supplementary Table S6 - EvidentialGene Summary Statistics for PacBio sequences. Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.2_assembly-contribution-count/reports/

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3363.1

Investigations: _I_STRT

Studies: SupplementaryInformation, _S_03_stCuSTr

Assays: Supplementary Information, _A_02.2_assembly-contribution-count

Download

Created: 26th Feb 2020 at 13:00, Last updated: 7th Apr 2020 at 13:49

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