_p_stRT
Overviewproject: _p_stRT
Short Name: stRT
Title: Solanum tuberosum Reference Transcriptomes
Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
pISA projects path: ../pISA-Projects
Local pISA-tree organisation: National Institute of Biology
pISA project creation date: 2019-10-22
pISA project creator: Maja Zagorscak, Ziva Ramsak, Marko Petek
Project funding code: This project was supported by the Slovenian Research Agency (grants P4-0165, J4-4165, J4-7636, J4-8228 and J4-9302), COST actions CA15110 (CHARME) and CA15109 (COSTNET).
Project coordinator: Kristina Gruden
Project partners: PacBio, Menlo Park, CA, USA; National Center for Genome Analysis and Support (NCGAS), Indiana University, Bloomington, USA; Laboratoire Génomique et Biotechnologie des Fruits, INRA-INP/ENSAT, Castanet-Tolosan, France
Project start date: December 2017
Project end date: October 2019
Principal investigator: Kristina Gruden
License: MIT, CC BY 4.0
Sharing permission: Public
Upload to FAIRDOMHub: Yes
RELATED FILES:
pISA/README.MD at projects · NIB-SI/pISA · GitHub https://fairdomhub.org/documents/350
/_PROJECT_METADATA.TXT https://fairdomhub.org/documents/329
/_p_stRT_TREE.TXT https://fairdomhub.org/documents/328
/presentations/README.MD https://fairdomhub.org/documents/335
/README.MD https://fairdomhub.org/documents/330
/reports/README.MD https://fairdomhub.org/documents/332
/Metadata_files https://fairdomhub.org/documents/331
Programme: NIBSys
SEEK ID: https://fairdomhub.org/projects/161
Funding codes:- J4-9302
- J4-4165
- CA15110
- J4-8228
- CA15109
- J4-7636
- P4-0165
Public web page: http://www.nib.si/eng/index.php/systems-biology
Organisms: Solanum tuberosum, Potato virus y
FAIRDOM PALs: No PALs for this Project
Project start date: 1st Dec 2017
Project end date: 1st Jan 2020
Related items
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, FAIRDOM user meeting, _p_stRT
Institutions: National Institute of Biology
https://orcid.org/0000-0001-5906-8569
Ph.D. in Biotechnology
Research associate at Department of Biotechnology and Systems Biology, National Institute of Biology
Projects: _p_stRT
Institutions: Indiana University Bloomington
Computational Biologist, Young Researcher at Department of Biotechnology and Systems Biology, National Institute of Biology NIB and PhD candidate in Statistics, Ljubljana, Slovenia
Investigation: _I_STRT
Short Name: STRT
Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Phenodata: ./phenodata_20191022.txt
pISA Investigation creation date: 2019-10-22
pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes
RELATED
...
Snapshots: No snapshots
Study: _S_04_stPanTr
Short Name: 04_stPanTr
Title: Solanum tuberosum Pan-Transcriptome
Description: Solanum tuberosum Pan-Transcriptome
Raw Data: _S_03_stCuSTr/
pISA Study creation date: 2019-10-22
pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes
RELATED FILES:
/reports/README.MD https://fairdomhub.org/documents/349
/_STUDY_METADATA.TXT https://fairdomhub.org/documents/348
/README.MD
...
Person responsible: Maja Zagorscak
Snapshots: Snapshot 1, Snapshot 2, Snapshot 3
Study: _S_03_stCuSTr
Short Name: 03_stCuSTr
Title: Solanum tuberosum Cultivar-Specific Transcriptomes
Description: Solanum tuberosum Cultivar-Specific Transcriptomes
Raw Data: ../_S_01_sequences/, ../_S_02_denovo/
pISA Study creation date: 2019-10-22
pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes
RELATED FILES:
/reports/README.MD https://fairdomhub.org/documents/346
/_STUDY_METADATA.TXT
...
Person responsible: Maja Zagorscak
Snapshots: No snapshots
Study: _S_02_denovo
Short Name: 02_denovo
Title: De novo assemblies
Description: De novo assemblies for cration of potato reference transcriptomes
Raw Data: ../_S_01_sequences/
pISA Study creation date: 2019-10-23
pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes
RELATED FILES:
/reports/README.MD https://fairdomhub.org/documents/343
/_STUDY_METADATA.TXT https://fairdomhub.org/documents/342
...
Study: _S_01_sequences
Short Name: 01_sequences
Title: NGS sequences for de novo assembly
Description: NGS sequences for de novo assembly; input for Study 02_denovo
Raw Data: see: ./reports/SupplementaryTableS1-Input_sequences_information.xlsx
pISA Study creation date: 2019-10-23
pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes
RELATED FILES:
/reports/README.MD
...
Assay: _A_01_evigene
Short Name: 01_evigene
Assay Class: DRY
Assay Type: evigene
Title: EvidentialGene tr2aacds.pl VERSION 2016.07.11
Description: See http://eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_02.1_BUSCO
Short Name: 02.1_BUSCO
Assay Class: DRY
Assay Type: BUSCO
Title: BUSCO on assemblies and tr2aacds output
Description: BUSCO on assemblies and tr2aacds output
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_02.3_InterProScan
Short Name: 02.3_InterProScan
Assay Class: DRY
Assay Type: InterProScan
Title: InterProScan on tr2aacds output
Description: InterProScan on tr2aacds output
pISA Assay creation date: 2019-10-22
pISA Assay creator: Marko Petek
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_02.2_assembly-contribution-count
Short Name: 02.2_assembly-contribution-count
Assay Class: DRY
Assay Type: count
Title: assembly contribution count
Description: assembly contribution count, input/output tr2aacds
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_02.4_STAR
Short Name: 02.4_STAR
Assay Class: DRY
Assay Type: STAR
Title: mapping reads back to evigene .tr output
Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map
pISA Assay creation date: 2019-10-22
pISA Assay creator: Marko Petek
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_02.5_STARlong_matchAnnot
Short Name: 02.5_STARlong_matchAnnot
Assay Class: DRY
Assay Type: matchAnnot
Title: potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations
Description: potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations
pISA Assay creation date: 2019-10-22
pISA Assay creator: Marko Petek
Phenodata: None
Featuredata: None
...
Assay: _A_02.6_TransRate
Short Name: 02.6_TransRate
Assay Class: DRY
Assay Type: TransRate
Title: TransRate stat on raw tr2aacds transcriptomes
Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: Nonde
Data: see ./input/path_to_files.txt
Assay: _A_02.7_VecScreen
Short Name: 02.7_VecScreen
Assay Class: DRY
Assay Type: VecScreen
Title: VecScreen on raw tr2aacds output
Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_02.8_DIAMOND
Short Name: 02.8_DIAMOND
Assay Class: DRY
Assay Type: DIAMOND
Title: DIAMOND on raw tr2aacds output
Description: DIAMOND on raw tr2aacds output, both .cds and .tr; including lost and found
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_04_TransRate
Short Name: 04_TransRate
Assay Class: DRY
Assay Type: TransRate
Title: TransRate post filtering and reassignment
Description: TransRate post filtering and reassignment
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_05_BUSCO
Short Name: 05_BUSCO
Assay Class: DRY
Assay Type: BUSCO
Title: BUSCO post filtering and reassignment
Description: BUSCO post filtering and reassignment
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_01_evigene_1_3cvs-gffmerged
Short Name: 01_evigene_1_3cvs-gffmerged
Assay Class: DRY
Assay Type: gffmerged
Title: tr2aacds on cv rep and gffmerged
Description: tr2aacds on cv rep and gffmerged
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_04-MSA
Short Name: 04-MSA
Assay Class: DRY
Assay Type: MSA
Title: Multiple sequence alignment, pantranscriptomes' paralogue clusters
Description: Multiple sequence alignment, pantranscriptomes' paralogue clusters
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Contributor: Maja Zagorscak
Biological problem addressed: Multiple sequence alignment
Snapshots: Snapshot 1
Assay: _A_05_BUSCO-Stat
Short Name: 05_BUSCO-Stat
Assay Class: DRY
Assay Type: Stat
Title: BUSCO plots
Description: BUSCO plots
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Analyst: Maja Zagorscak
Phenodata: None
Featuredata:
Data:
Assay: _A_03_BUSCO_1_3cvs-gffmerged
Short Name: 03_BUSCO_1_3cvs-gffmerged
Assay Class: DRY
Assay Type: gffmerged
Title: BUSCO on pantranscriptome
Description: BUSCO on pantranscriptome
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Assay: _A_02_components_1_3cvs-gffmerged
Short Name: 02_components_1_3cvs-gffmerged
Assay Class: DRY
Assay Type: gffmerged
Title: paralogue clusters on pantranscriptome
Description: paralogue clusters on pantranscriptome
pISA Assay creation date: 2019-10-22
pISA Assay creator: Ziva Ramsak
Phenodata: None
Featuredata:
Data:
Assay: _A_03.2_components
Short Name: 03.2_components
Assay Class: DRY
Assay Type: components
Title: Components: tr2aacds headers, cdhit-2d
Description: Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters
pISA Assay creation date: 2019-10-22
pISA Assay creator: Ziva Ramsak
Phenodata: None
Featuredata:
Data:
Assay: _A_03.1_filtering
Short Name: 03.1_filtering
Assay Class: DRY
Assay Type: filtering
Title: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
Description: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Download
_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA
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
Contributor: Maja Zagorscak
Number of transcripts from de novo assemblies contributing to breeding clone PW363, 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, Sdn - SPAdes.
Number of transcripts from de novo assemblies contributing to cultivar Rywal, 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, Sdn - SPAdes, PBdn - PacBio.
Supplementary Table S3
Désirée biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Désirée.
Supplementary Table S4
PW363 biological evidence filtering results. Output of 1st filtering step by biological evidence for breeding clone PW363.
Supplementary Table S5
Rywal biological evidence filtering results. Output of 1st filtering step by biological evidence for cv. Rywal.
Supplementary HTML 1
Multiple sequence alignments using MAFFT v7.271 and MView v1.65.
Paralogue cluster on representative and alternative sequences, at least one from each of the four genotypes. Clusters containing 8-16 sequences.
Abstract (Expand)
Authors: Marko Petek, Maja Zagorscak, Ziva Ramsak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll Rius, Kristina Gruden
Date Published: No date defined
Journal: Not specified
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_01_sequences
Creators: Maja Zagorscak, Marko Petek
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_01_sequences
Creators: Maja Zagorscak, Marko Petek
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_02_denovo
Creators: Maja Zagorscak, Marko Petek
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_02_denovo
Creators: Maja Zagorscak, Marko Petek
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_03_stCuSTr
Creators: Maja Zagorscak, Ziva Ramsak
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_03_stCuSTr
Creators: Maja Zagorscak, Ziva Ramsak
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr
Creators: Maja Zagorscak, Ziva Ramsak
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr
Creators: Maja Zagorscak, Ziva Ramsak
Contributor: Maja Zagorscak
pISA-tree: Standard project directory tree (ISA-tab compliant) - NIB-SI/pISA
https://github.com/NIB-SI/pISA/
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA
Creator: Maja Zagorscak
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA
Creator: Maja Zagorscak
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA
Creator: Maja Zagorscak
Contributor: Maja Zagorscak
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
