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256 Data files visible to you, out of a total of 272

/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

Download

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

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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

Download

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

Download

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

/reports/cv_group-Rplot.pdf

_p_stRT

No description specified

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 24th Mar 2020 at 12:35, Last updated: 24th Mar 2020 at 12:35

/reports/cvID_group-Rplot.pdf

_p_stRT

No description specified

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_02_cdhit_3cvs-GFFmerged

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Created: 24th Mar 2020 at 12:33

/output/PGSC_DM_v3.4_transcript-update_representative_transrate_usingReference/PGSC_DM_v3.4_transcript-update_representative/contigs.csv

_p_stRT

No description specified

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_06_tr_rep-transrate

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Created: 23rd Mar 2020 at 18:08

/reports/SupplementaryFile3.html

_p_stRT

Supplementary File 3 - Taxonomi cclassification of Désirée, PW363 and Rywal representative transcripts. Sequences were classified using Centrifuge and Sankey plots were generated using Pavian. Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_08_cdhit_centrifuge_3cvs-GFFmerged

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3509.1

Investigations: _I_STRT

Studies: SupplementaryInformation, _S_04_stPanTr

Assays: Supplementary Information, _A_08_centrifuge_3cvs-GFFmerged

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Created: 20th Mar 2020 at 19:08, Last updated: 23rd Mar 2020 at 16:55

/reports/SupplementaryFile2.html

_p_stRT

Supplementary File 2 - Multiple sequence alignments using ClustalOmega v1.2.1 or MAFFT v7.271 and MView v1.66. Paralogue clusters on representative and alternative sequences, at least one from each of the four genotypes. Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_05_MSA_3cvs-GFFmerged

Creator: Maja Zagorscak

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3691.1

Investigations: _I_STRT

Studies: SupplementaryInformation, _S_04_stPanTr

Assays: Supplementary Information, _A_05_MSA_3cvs-GFFmerged

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Created: 23rd Mar 2020 at 15:54, Last updated: 23rd Mar 2020 at 15:59

/input/path_to_files.txt

_p_stRT