Data files

What is a Data file?
3939 Data files visible to you, out of a total of 5920
/output/alt.cds.IDs

_p_stRT/_I_STRT/_S_04_stPanTr/_A_03_components_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/output/alt.aa.IDs

_p_stRT/_I_STRT/_S_04_stPanTr/_A_03_components_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/scripts/commands-components_1_3cvs-gffmerged.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_03_components_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/reports/SupplementaryFigure4.pdf

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

Download
/reports/SupplementaryTableS7

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

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

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/output/VennDiagrams/stPanTr_geneCount_weak-components_repOnly.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

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

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

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

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

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

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

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

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/output/VennDiagrams/stPanTr_geneCount_weak-components_rep_perc.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/output/VennDiagrams/stPanTr_geneCount_weak-components_rep.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/output/VennDiagrams/stPanTr_geneCount_weak-components.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/output/stPanTr-clusters.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

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

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

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

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

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

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/output/annot.alias.cds.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/output/annot.alias.aa.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/output/5cv_weak-components_withAnnotation.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/output/5cv_weak-components.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/scripts/04_summary_stPanTr_v4.html

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
/scripts/03_stPanTr_components_all.html

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

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

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

Creator: Andrej Blejec

Submitters: Andrej Blejec, Maja Zagorscak

Download
Influx simulation data for "Charting the metabolic landscape of the facultative methylotroph Bacillus methanolicus"

This archive contains influx software input, output and model files used to estimate in vivo reaction rates of B. methanolicus on methanol, mannitol, and arabitol for the paper "Charting the metabolic landscape of the facultative methylotroph Bacillus methanolicus".

Creator: Baudoin Delépine

Submitter: Baudoin Delépine

Download
/reports/SupplementaryTableS1

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

Download
/reports/SupplementaryTableS2

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

Download
/reports/SupplementaryFigure1.pdf

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

Download
SupplementaryFile1

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

Download
Powered by
 (v.1.16.0-pre)
About FAIRDOMHub | Funding and Programmes | Credits | Terms & Conditions | Imprint | Cookie preferences
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH