_p_stRT

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project: _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:

P4-0165
J4-7636
J4-4165
J4-8228
J4-9302
CA15110
CA15109

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

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Anna Coll Rius

Projects: _p_stRT

Institutions: National Institute of Biology

https://orcid.org/0000-0003-0672-1530

Kristina Gruden

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, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato

Institutions: National Institute of Biology

https://orcid.org/0000-0001-5906-8569

Expertise: Plant biology, immune signaling, transcriptional regulation

Tools: Transcriptomics, Molecular Biology, Systems Biology, network theory, Data Integration

Marko Petek

PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology

Sheri Sanders

Projects: _p_stRT

Institutions: Indiana University Bloomington

Špela Tomaž

Projects: _p_stRT

Institutions: National Institute of Biology

Alan Williams

Projects: FAIRDOM, FAIRDOM Community Workers, _p_stRT

Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester

https://orcid.org/0000-0003-3156-2105

Expertise: Synthetic Biology

Tools: Workflows, Web services

Maja Zagorscak

Projects: pISA-tree, HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, tst, tst2

Institutions: National Institute of Biology, tst

https://orcid.org/0000-0002-1669-6482

Computational Biologist and Biostatistician at Department of Biotechnology and Systems Biology, National Institute of Biology (NIB)

Advanced Programmes list for this Project with search and filtering ...

NIBSys

National Institute of Biology, Department of Biotechnology and Systems Biology projects

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, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground

Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology

Advanced Institutions list for this Project with search and filtering ...

Indiana University Bloomington

Country: United States

City: Bloomington

Web page: https://www.indiana.edu

Manchester Centre for Integrative Systems Biology, University of Manchester

Country: United Kingdom

City: Manchester

Web page: http://www.mib.ac.uk/

National Institute of Biology

Country: Slovenia

City: Ljubljana

Web page: http://www.nib.si

Advanced Investigations list for this Project with search and filtering ...

_I_STRT

_p_stRT

(Show All)

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 ...

Created: 24th Oct 2019 at 16:36, Last updated: 26th Nov 2019 at 10:37

Advanced Studies list for this Project with search and filtering ...

_S_04_stPanTr

_p_stRT

Short Name: 04_stPanTr Title: Solanum tuberosum Pan-Transcriptome Description: Solanum tuberosum Pan-Transcriptome Raw Data: pISA Study creation date: 2019-10-22 pISA Study creator: Maja Zagorscak Principal investigator: Kristina Gruden License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Submitter: Andrej Blejec

Investigation: _I_STRT

Assays: _A_01_GC_content-count, _A_02_cdhit_3cvs-GFFmerged, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged

Snapshots: No snapshots

Created: 18th Mar 2020 at 21:44

SupplementaryInformation

_p_stRT

Supplementary Information linked together

Submitter: Maja Zagorscak

Investigation: _I_STRT

Assays: Supplementary Information

Snapshots: No snapshots

Created: 13th Mar 2020 at 19:23, Last updated: 13th Mar 2020 at 19:23

_S_03_stCuSTr

_p_stRT

(Show All)

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 ...

Submitter: Maja Zagorscak

Investigation: _I_STRT

Assays: _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _A_02.3_InterProScan, _A_02.4_STAR, _A_02.5_STARlong_matchAnnot, _A_02.6_TransRate, _A_02.7_VecScreen, _A_02.8_DIAMOND, _A_03.1_filtering, _A_03.2_components, _A_04_TransRate, _A_05_BUSCO

Snapshots: No snapshots

Created: 24th Oct 2019 at 16:40, Last updated: 26th Nov 2019 at 10:36

_S_02_denovo

_p_stRT

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 ...

Submitter: Maja Zagorscak

Investigation: _I_STRT

Assays: No Assays

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.study.668.1

Created: 24th Oct 2019 at 16:39, Last updated: 26th Nov 2019 at 10:35

_S_01_sequences

_p_stRT

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 ...

Submitter: Maja Zagorscak

Investigation: _I_STRT

Assays: No Assays

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.study.667.1

Created: 24th Oct 2019 at 16:38, Last updated: 26th Nov 2019 at 10:35

Showing 20 out of a possible 23 items Advanced Assays list for this Project with search and filtering ...

_A_01_evigene

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Integration

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_Rywal.tar.gz, /output/output.tar, /scripts/01_run_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh

Snapshots: Snapshot 1

Created: 7th Nov 2019 at 16:54, Last updated: 16th Nov 2019 at 14:21

_A_02.1_BUSCO

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1162.1

Created: 7th Nov 2019 at 16:57, Last updated: 16th Nov 2019 at 13:40

_A_02.2_assembly-contribution-count

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_Desiree.tar.gz, /intermediate_PW363.tar.gz, /intermediate_Rywal.tar.gz, /output/output.tar, /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /reports/SupplementaryFigure3.pdf, /reports/SupplementaryTableS6, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1163.1

Created: 7th Nov 2019 at 17:04, Last updated: 26th Feb 2020 at 14:00

_A_02.3_InterProScan

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate/intermediate.tar, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1164.1

Created: 7th Nov 2019 at 17:46, Last updated: 16th Nov 2019 at 13:35

_A_02.4_STAR

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/samtoolsCoverage.zip, /reports/summaryCounts&SJ.xlsx, /scripts/STAR_commands.txt

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1165.1

Created: 7th Nov 2019 at 17:48, Last updated: 2nd Jun 2020 at 15:42

_A_02.5_STARlong_matchAnnot

_p_stRT

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 ...

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_1_STARlong-logs-n-SJ.tar.gz, /output/output_2_matchAnnot-parsed-txt.tar.gz, /scripts/STARlongMatchAnnot_commands_ENCODE_den...

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1166.1

Created: 7th Nov 2019 at 17:50, Last updated: 16th Nov 2019 at 12:55

_A_02.6_TransRate

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1167.1

Created: 7th Nov 2019 at 17:54, Last updated: 16th Nov 2019 at 12:45

_A_02.7_VecScreen

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate.tar.gz, /output/Desiree_vecscreen.tsv, /output/PW363_vecscreen.tsv, /output/Rywal_vecscreen.tsv, /scripts/01_get_input.sh, /scripts/02_VecScreenPlus_blastn.sh, /scripts/ENCH_sumablastplus.pl

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1168.1

Created: 7th Nov 2019 at 17:58, Last updated: 16th Nov 2019 at 12:37

_A_02.8_DIAMOND

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1169.1

Created: 7th Nov 2019 at 18:02, Last updated: 16th Nov 2019 at 12:28

_A_03.1_filtering

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate/intermediate.tar, /output/Desiree_tr.cds.tsv.gz, /output/PW363_tr.cds.tsv.gz, /output/Rywal_tr.cds.tsv.gz, /output/other/output_full.tar.gz, /output/other/output_summary.tar.gz, /reports/03.1_Rywal_combo_withFiltering.html, /reports/03.2_PW363_combo_withFiltering.html, /reports/03.3_Desiree_combo_withFiltering.html, /reports/SupplementaryTableS3, /reports/SupplementaryTableS4, /reports/SupplementaryTableS5, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1170.1

Created: 7th Nov 2019 at 18:04, Last updated: 18th Mar 2020 at 19:37

_A_03.2_components

_p_stRT

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:

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_4_cdhit-2d.tar.gz, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1171.1

Created: 7th Nov 2019 at 18:06, Last updated: 15th Nov 2019 at 21:07

_A_04_TransRate

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output.tar, /scripts/run_TransRate_commands.sh

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1172.1

Created: 7th Nov 2019 at 18:09, Last updated: 16th Nov 2019 at 12:22

_A_05_BUSCO

_p_stRT

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

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar, /transfer/transfer.zip

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1173.1

Created: 7th Nov 2019 at 18:11, Last updated: 16th Nov 2019 at 12:08

Supplementary Information

_p_stRT

Supplementary Information linked together

Submitter: Maja Zagorscak

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: SupplementaryInformation

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /reports/SupplementaryFigure3.pdf, /reports/SupplementaryFigure4.pdf, /reports/SupplementaryFile2.html, /reports/SupplementaryFile3.html, /reports/SupplementaryTableS1, /reports/SupplementaryTableS2, /reports/SupplementaryTableS3, /reports/SupplementaryTableS4, /reports/SupplementaryTableS5, /reports/SupplementaryTableS6, /reports/SupplementaryTableS7, /reports/SupplementaryTableS8, SupplementaryFile1

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1261.1

Created: 13th Mar 2020 at 19:24, Last updated: 8th Apr 2020 at 18:30

_A_02_cdhit_3cvs-GFFmerged

_p_stRT

Short Name: cdhit_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC Description: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC pISA Assay creation date: 2020-03-09 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.1263.2

Created: 18th Mar 2020 at 21:44, Last updated: 5th May 2022 at 01:36

_A_01_GC_content-count

_p_stRT

Short Name: 01_GC_content-count Assay Class: DRY Assay Type: count Title: GC content and sequence length Description: A, C, T, G content and sequence length pISA Assay creation date: 2020-03-09 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data: ../input/path_to_files.txt

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/Solanum_tuberosum-ITAG_DM_v1_cds.fasta, /input/Solanum_tuberosum_PGSC_merged.fasta, /input/StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_gf..., /output/Solanum_tuberosum-ITAG_DM_v1_cds_GC.txt, /output/Solanum_tuberosum_PGSC_merged.CDS_GC.txt, /output/StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_g..., /scripts/GC_content.py, /scripts/tab_to_fasta.py and 12 hidden items

Snapshots: No snapshots

Created: 19th Mar 2020 at 11:02, Last updated: 5th May 2022 at 01:34

_A_04_BUSCO_3cvs-GFFmerged

_p_stRT

Short Name: 04_BUSCO_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: BUSCOs Description: BUSCO on ITAG, PGSC, ITAG/PGSC merged, pan-transcriptome representatives, pan-transcriptome alternatives, and pan-transcriptome pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Snapshots: No snapshots

Created: 19th Mar 2020 at 11:13, Last updated: 6th Apr 2020 at 01:46

_A_07_Desiree-mapping

_p_stRT

Short Name: 07_Desiree-mapping Assay Class: DRY Assay Type: mapping Title: Desiree mapping Description: Mapping of Desiree samples (drought stress) to Desiree and Phureja transcriptomes pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Snapshots: No snapshots

Created: 19th Mar 2020 at 11:38, Last updated: 12th Apr 2020 at 11:51

_A_09_annotation-GFFmerged

_p_stRT

Short Name: 09_annotation-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: Pan-transcriptome fasta files annotation Description: Annotation of pan-transcriptome and re-annotation of cultivar-specific transcriptomes pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.1268.2

Created: 19th Mar 2020 at 11:41, Last updated: 9th Apr 2020 at 12:14

_A_03_components_3cvs-GFFmerged

_p_stRT

Short Name: 03_components_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: components Description: representative and alternative pan-transcriptome CDS and polypeptide fasta files pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/Solanum_tuberosum_PGSC_DM_v4.04_CDS-to-..., /output/alt.aa.IDs, /output/alt.cds.IDs, /output/rep.aa.IDs, /output/rep.cds.IDs, /scripts/commands-components_1_3cvs-gffmerged.txt

Snapshots: No snapshots

Created: 19th Mar 2020 at 11:55, Last updated: 6th Apr 2020 at 01:48

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