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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
Related items
- People (9)
- Institutions (3)
- Investigations (1)
- Studies (5)
- Assays (23)
- Data files (338)
- Publications (1)
- Documents (120)
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

Ph.D. in Biotechnology
Research associate at Department of Biotechnology and Systems Biology, National Institute of Biology
Projects: _p_stRT
Institutions: Indiana University Bloomington
Projects: _p_stRT
Institutions: National Institute of Biology
Projects: FAIRDOM, FAIRDOM Templates, FAIRDOM Community Workers, _p_stRT
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester

Expertise: Synthetic Biology
Tools: Workflows, Web services
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
Institutions: National Institute of Biology

Roles: PhD Student
Expertise: Molecular Biology, Statistics, Bioinformatics, Mathematical and statistical modeling, Programming, Data analysisMathematical modellingBioinformaticsSystems biology, Data Management, Data analysis, Visualization, Data Integration, Computational Biology
Tools: Bioinformatics, Computational and theoretical biology, Computational Systems Biology, Data Management, Databases, Dynamic modelling, Molecular Biology, Python, R, Systems Biology, Data Integration
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
Studies: SupplementaryInformation, _S_01_sequences, _S_02_denovo, _S_03_stCuSTr, _S_04_stPanTr
Assays: Supplementary Information, _A_01_GC_content-count, _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_02_cdhit_3cvs-GFFmerged, _A_03.1_filtering, _A_03.2_components, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_04_TransRate, _A_05_BUSCO, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
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
Person responsible: Andrej Blejec
Snapshots: No snapshots
Supplementary Information linked together
Person responsible: Maja Zagorscak
Snapshots: No snapshots
Investigation: _I_STRT
Assays: Supplementary Information
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
...
Investigation: _I_STRT
Assays: No Assays
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
...
Investigation: _I_STRT
Assays: No Assays
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
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
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:
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/PGSC_DM_v3.4_transcript-update_represent..., /intermediate/Desiree/chrLength.txt, /intermediate/Desiree/chrName.txt, /intermediate/Desiree/chrNameLength.txt, /intermediate/Desiree/chrStart.txt, /intermediate/Desiree/genomeParameters.txt, /intermediate/PGSC/chrLength.txt, /intermediate/PGSC/chrName.txt, /intermediate/PGSC/chrNameLength.txt, /intermediate/PGSC/chrStart.txt, /intermediate/PGSC/genomeParameters.txt, /intermediate/gff-merged/chrLength.txt, /intermediate/gff-merged/chrName.txt, /intermediate/gff-merged/chrNameLength.txt, /intermediate/gff-merged/chrStart.txt, /intermediate/gff-merged/genomeParameters.txt, /intermediate/indexDesiree.log, /intermediate/indexGFFmerged.log, /intermediate/indexPGSC.log, /output/Desiree_SRR10416847/Log.final.out, /output/Desiree_SRR10416847/Log.out, /output/Desiree_SRR10416847/Log.progress.out, /output/Desiree_SRR10416847/SJ.out.tab, /output/Desiree_SRR10416848/Log.final.out, /output/Desiree_SRR10416848/Log.out, /output/Desiree_SRR10416848/Log.progress.out, /output/Desiree_SRR10416848/SJ.out.tab, /output/Desiree_SRR10416849/Log.final.out, /output/Desiree_SRR10416849/Log.out, /output/Desiree_SRR10416849/Log.progress.out, /output/Desiree_SRR10416849/SJ.out.tab, /output/Desiree_drought123/Desiree_Aligned.sort..., /output/Desiree_drought123/Log.final.out, /output/Desiree_drought123/Log.out, /output/Desiree_drought123/Log.progress.out, /output/Desiree_drought123/SJ.out.tab, /output/PGSC_SRR10416847/Log.final.out, /output/PGSC_SRR10416847/Log.out, /output/PGSC_SRR10416847/Log.progress.out, /output/PGSC_SRR10416847/SJ.out.tab, /output/PGSC_SRR10416848/Log.final.out, /output/PGSC_SRR10416848/Log.out, /output/PGSC_SRR10416848/Log.progress.out, /output/PGSC_SRR10416848/SJ.out.tab, /output/PGSC_SRR10416849/Log.final.out, /output/PGSC_SRR10416849/Log.out, /output/PGSC_SRR10416849/Log.progress.out, /output/PGSC_SRR10416849/SJ.out.tab, /output/PGSC_drought123/DM_Aligned.sortedByCoor..., /output/PGSC_drought123/Log.final.out, /output/PGSC_drought123/Log.out, /output/PGSC_drought123/Log.progress.out, /output/PGSC_drought123/SJ.out.tab, /output/gff-merged_SRR10416847/Log.final.out, /output/gff-merged_SRR10416847/Log.out, /output/gff-merged_SRR10416847/Log.progress.out, /output/gff-merged_SRR10416847/SJ.out.tab, /output/gff-merged_SRR10416848/Log.final.out, /output/gff-merged_SRR10416848/Log.out, /output/gff-merged_SRR10416848/Log.progress.out, /output/gff-merged_SRR10416848/SJ.out.tab, /output/gff-merged_SRR10416849/Log.final.out, /output/gff-merged_SRR10416849/Log.out, /output/gff-merged_SRR10416849/Log.progress.out, /output/gff-merged_SRR10416849/SJ.out.tab, /output/gff-merged_drought123/Log.final.out, /output/gff-merged_drought123/Log.out, /output/gff-merged_drought123/Log.progress.out, /output/gff-merged_drought123/SJ.out.tab, /reports/SupplementaryTableS8, /scripts/00_wget.txt, /scripts/01_index_ref.txt, /scripts/02_map.txt, /scripts/03_clean-dir.txt
Short Name: 05_MSA_3cvs-GFFmerged
Assay Class: DRY
Assay Type: GFFmerged
Title: MSA 3cv and GFF-merged
Description: Multiple sequence alignment of Desiree, PW363, Rywal and ITAG/PGSC
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
Snapshots: Snapshot 1, Snapshot 2
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/folderWithIds/test.IDs1, /input/folderWithIds/test.IDs2, /input/my.test.aa.fasta, /input/path_to_files.txt, /reports/SupplementaryFile2.html, /scripts/MSA-commands.txt, /scripts/MSA.py, /scripts/print.sh
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
Snapshots: Snapshot 1, Snapshot 2
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/Solanum_tuberosum_ITAG_DM_v1_description..., /input/Solanum_tuberosum_PGSC_DM_v4.04_converte..., /input/StPGSC4.04n_seq_4_PGSC-p-rep_ITAG-pep_gf..., /input/path_to_files.txt, /intermediate/singletons.DM.seqID.txt, /intermediate/singletons.seqID.txt, /intermediate/singletons.tetra.seqID.txt, /intermediate/stCuSTr_cds_repAlt_cdhitEST-conda..., /intermediate/stPanTr_aa_singletons_DM_on_tetra..., /intermediate/stPanTr_aa_singletons_tetra_on_DM..., /output/5cv_weak-components.txt, /output/5cv_weak-components_withAnnotation.tsv, /output/VennDiagrams/stPanTr+stCuSTr_geneCount_..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/annot.alias.aa.tsv, /output/annot.alias.cds.tsv, /output/cdhit-est_rep-alt_aS.75_c.90_pairs.tsv, /output/cdhit-est_representativesMatched_aS.75_..., /output/cdhit-est_singletons_aS.75_c.90.tsv, /output/stPanTr-clusters.tsv, /output/trueSingle.DM.ID, /output/trueSingle.polyploid.ID, /reports/SupplementaryFigure4.pdf, /reports/SupplementaryTableS7, /reports/cvID_group-Rplot.pdf, /reports/cv_group-Rplot.pdf, /scripts/01.1_commands-CDHIT-EST.txt, /scripts/01.2_commands-CDHIT-2D.txt, /scripts/02_cd-hit-est_cdhit-2d.html, /scripts/03_stPanTr_components_all.html, /scripts/04_summary_stPanTr_v4.html
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
Snapshots: Snapshot 1, Snapshot 2
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /output/annot_stCuSTr-D_aa_all.zip, /output/annot_stCuSTr-D_aa_representatives.zip, /output/annot_stCuSTr-D_cds_all.zip, /output/annot_stCuSTr-D_cds_representatives.zip, /output/annot_stCuSTr-D_tr_all.zip, /output/annot_stCuSTr-D_tr_representatives.zip, /output/annot_stCuSTr-P_aa_all.zip, /output/annot_stCuSTr-P_aa_representatives.zip, /output/annot_stCuSTr-P_cds_all.zip, /output/annot_stCuSTr-P_cds_representatives.zip, /output/annot_stCuSTr-P_tr_all.zip, /output/annot_stCuSTr-P_tr_representatives.zip, /output/annot_stCuSTr-R_aa_all.zip, /output/annot_stCuSTr-R_aa_representatives.zip, /output/annot_stCuSTr-R_cds_all.zip, /output/annot_stCuSTr-R_cds_representatives.zip, /output/annot_stCuSTr-R_tr_all.zip, /output/annot_stCuSTr-R_tr_representatives.zip, /output/annot_stPanTr.aa.zip, /output/annot_stPanTr.cds.zip, /output/annot_stPanTr_rep.aa.zip, /output/annot_stPanTr_rep.cds.zip, /scripts/annotate.sh
Supplementary Information linked together
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
Short Name: 08_centrifuge_3cvs-GFFmerged
Assay Class: DRY
Assay Type: GFFmerged
Title: Centrigufe pan-transcriptome sequence classification
Description: Classify cv rep transcripts and pan-transcriptome singletons based on taxonomy
pISA Assay creation date: 2020-03-11
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data:
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /input/taxdmp.tgz, /input/trueSingle.DM.ID, /input/trueSingle.polyploid.ID, /intermediate/trueSingle.DM.cds.fasta, /intermediate/trueSingle.polyploid.cds.fasta, /intermediate/trueSingle.polyploid.tr.fasta, /output/Desiree_centrifuge.txt, /output/Desiree_kreport.txt, /output/Desiree_report.txt, /output/PW363_centrifuge.txt, /output/PW363_kreport.txt, /output/PW363_report.txt, /output/Rywal_centrifuge.txt, /output/Rywal_kreport.txt, /output/Rywal_report.txt, /output/Tetraploid_transcriptomes-report.html, /output/Uploaded_sample_set-report.html, /output/pavian_class_summary_No.csv, /output/pavian_class_summary_perc.csv, /output/sankey-Desiree.html, /output/sankey-PW363.html, /output/sankey-Rywal.html, /output/sankey-trueSingle.DM.cds.html, /output/sankey-trueSingle.polyploid.cds.html, /output/sankey-trueSingle.polyploid.tr.html, /output/trueSingle.DM.cds_centrifuge.txt, /output/trueSingle.DM.cds_kreport.txt, /output/trueSingle.DM.cds_report.txt, /output/trueSingle.polyploid.cds_centrifuge.txt, /output/trueSingle.polyploid.cds_kreport.txt, /output/trueSingle.polyploid.cds_report.txt, /output/trueSingle.polyploid.tr_centrifuge.txt, /output/trueSingle.polyploid.tr_kreport.txt, /output/trueSingle.polyploid.tr_report.txt, /reports/SupplementaryFile3.html, /scripts/01_prepareFasta.sh, /scripts/02_centrifuge_commands.txt
Short Name: 06_tr_rep-transrate
Assay Class: DRY
Assay Type: transrate
Title: Cultivar representative transcriptome transrate
Description: Transrate on cultivar specific representatives, GFF merged as a reference for CRRB
pISA Assay creation date: 2020-03-11
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data:
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/PGSC_DM_v3.4_transcript-update_represent..., /input/path_to_files.txt, /output/PGSC_DM_v3.4_transcript-update_represen..., /output/PGSC_DM_v3.4_transcript-update_represen..., /output/PGSC_DM_v3.4_transcript-update_represen..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /scripts/run_TransRate_commands.sh
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:
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
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:
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /output/BUSCO_stPanTr_embryophyta_odb9.tsv, /output/BUSCO_stPanTr_solanaceae_odb10.tsv, /output/short_summary_BUSCO_Solanum_tuberosum-I..., /output/short_summary_BUSCO_Solanum_tuberosum-I..., /output/short_summary_BUSCO_Solanum_tuberosum-P..., /output/short_summary_BUSCO_Solanum_tuberosum-P..., /output/short_summary_BUSCO_Solanum_tuberosum_P..., /output/short_summary_BUSCO_Solanum_tuberosum_P..., /output/short_summary_BUSCO_Solanum_tuberosum_P..., /output/short_summary_BUSCO_Solanum_tuberosum_P..., /output/short_summary_BUSCO_StPGSC4.04n_seq_4_P..., /output/short_summary_BUSCO_StPGSC4.04n_seq_4_P..., /output/short_summary_BUSCO_stPanTr.aa.fasta_em..., /output/short_summary_BUSCO_stPanTr.aa.fasta_so..., /output/short_summary_BUSCO_stPanTr_alt.aa.fast..., /output/short_summary_BUSCO_stPanTr_alt.aa.fast..., /output/short_summary_BUSCO_stPanTr_rep.aa.fast..., /output/short_summary_BUSCO_stPanTr_rep.aa.fast..., /scripts/01_run_BUSCO_commands.sh, /scripts/02_BUSCO_plots.html
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
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
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
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
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
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
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
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
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
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
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
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
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
...
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...
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
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
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
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
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
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
coverage and uniquely mapped spliced reads summary
samtools coverage
https://www.htslib.org/doc/samtools-coverage.html
Creator: Maja Zagorscak
Submitter: Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
Abstract (Expand)
Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/845818
Citation: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Creator: Sheri Sanders
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Description of Tags found on transcript headers
https://blogs.iu.edu/ncgas/2018/12/17/how-evigene-works/#step3
Creator: Sheri Sanders
Submitter: Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
Creator: Maja Zagorscak
Submitter: Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_04_stPanTr/_A_09_annotation-GFFmerged
Creator: Andrej Blejec
Submitter: Andrej Blejec