_p_stRT

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

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

Ph.D. 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 Templates, 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

Institutions: National Institute of Biology

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

Computational Biologist, Young Researcher at Department of Biotechnology and Systems Biology, National Institute of Biology NIB and PhD candidate in Statistics, Ljubljana, Slovenia

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

_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

_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

Person responsible: Andrej Blejec

Snapshots: No snapshots

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

Created: 18th Mar 2020 at 21:44

SupplementaryInformation

_p_stRT

Supplementary Information linked together

Person responsible: Maja Zagorscak

Snapshots: No snapshots

Investigation: _I_STRT

Assays: Supplementary Information

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
...

Person responsible: Maja Zagorscak

Snapshots: No snapshots

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

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
...

Person responsible: Marko Petek

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.study.668.1

Investigation: _I_STRT

Assays: No Assays

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
...

Person responsible: Marko Petek

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.study.667.1

Investigation: _I_STRT

Assays: No Assays

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

_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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1165.1

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

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

_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

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

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

_A_05_MSA_3cvs-GFFmerged

_p_stRT

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

DOI: 10.15490/fairdomhub.1.assay.1270.2

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

Created: 19th Mar 2020 at 11:58, Last updated: 12th Apr 2020 at 11:42

_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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.1263.2

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Created: 18th Mar 2020 at 21:44, Last updated: 11th Apr 2020 at 00:14

_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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.1268.2

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

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

Supplementary Information

_p_stRT

Supplementary Information linked together

Submitter: Maja Zagorscak

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1261.1

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

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

_A_08_centrifuge_3cvs-GFFmerged

_p_stRT

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:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Created: 22nd Mar 2020 at 00:09, Last updated: 6th Apr 2020 at 01:50

_A_06_tr_rep-transrate

_p_stRT

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:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Created: 19th Mar 2020 at 12:00, Last updated: 6th Apr 2020 at 01:49

_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

Snapshots: No snapshots

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

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

_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

Snapshots: No snapshots

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

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

_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

Snapshots: No snapshots

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

Created: 19th Mar 2020 at 11:02, Last updated: 6th Apr 2020 at 01:45

_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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1170.1

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

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

_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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1163.1

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

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

_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

Snapshots: Snapshot 1

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

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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1162.1

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

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

_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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1164.1

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

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

_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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1166.1

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...

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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1167.1

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

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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1168.1

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

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

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1169.1

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

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

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