_I_STRT-1

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Investigation: _I_STRT\n Short Name: STRT\n 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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes

SEEK ID: https://testing.sysmo-db.org/investigations/125

Projects: _p_stRT

Investigation position:

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Creators and Submitter

Creator

Andrej Blejec

Submitter

Andrej Blejec

Activity

Views: 625

Created: 6th Nov 2019 at 22:25

Last updated: 13th Nov 2019 at 22:21

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People (1)
Programmes (1)
Projects (1)
Studies (4)
Assays (24)
Data files (380)
Documents (95)

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Andrej Blejec

Institutions: National Institute of Biology, NIB, <script>alert('xss-institution-title')</script> & Test Institution

https://orcid.org/0000-0001-7484-6031

Expertise: STatistics, R, Programming, Data Management

Tools: R, API

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pISA-tree

Local data management; testing uploading/downloading using API

Web page: Not specified

Advanced Projects list for this Investigation with search and filtering

_p_stRT

Test project for upload

Programme: pISA-tree

Public web page: Not specified

Organisms: Not specified

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_S_04_stPanTr

_p_stRT

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Andrej Blejec

/transfer/evg_out.tsv _p_stRT/_I_STRT/_S_03_stCuSTr/_A_05_BUSCO

Submitter: Andrej Blejec

Investigation: _I_STRT-1

Assays: _A_01_evigene_1_3cvs-gffmerged, _A_02_components_1_3cvs-gffmerged, _A_03_BUSCO_1_3cvs-gffmerged, _A_04-MSA, _A_05_BUSCO-Stat, _A_05_BUSCO-Stat-old, _A__S_04_stPanTr-files

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:16

_S_02_denovo

_p_stRT

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Andrej Blejec

/reports/SupplementaryTableS1-Input_sequences_information.xlsx _p_stRT/_I_STRT/_S_01_sequences/_A__S_01_sequences-files

Submitter: Andrej Blejec

Investigation: _I_STRT-1

Assays: _A__S_02_denovo-files

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:04

_S_01_sequences

_p_stRT

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Andrej Blejec

Solanum tuberosum Reference Transcriptomes Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Submitter: Andrej Blejec

Investigation: _I_STRT-1

Assays: _A__S_01_sequences-files

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:04

_S_03_stCuSTr

_p_stRT

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Andrej Blejec

No description specified

Submitter: Andrej Blejec

Investigation: _I_STRT-1

Assays: _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _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, _A__S_03_stCuSTr-files

Snapshots: No snapshots

Created: 6th Nov 2019 at 22:28

Showing 20 out of a possible 24 Assays Advanced Assays list for this Investigation with search and filtering

_A_02.8_DIAMOND

_p_stRT

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Andrej Blejec

No description specified

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

SOPs: No SOPs

Snapshots: No snapshots

Created: 7th Nov 2019 at 09:18, Last updated: 10th Nov 2019 at 23:12

_A_02.4_STAR

_p_stRT

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Andrej Blejec

No description specified

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

SOPs: No SOPs

Data files: /_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.4_STAR/sho..., /input/path_to_files.txt, /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/output_STAR_logs-n-SJ.tar.gz, /scripts/STAR_commands.txt, /scripts/STAR_commands.txt

Snapshots: No snapshots

Created: 7th Nov 2019 at 10:03, Last updated: 13th Nov 2019 at 22:29

_A_01_evigene

_p_stRT

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Andrej Blejec

EvidentialGene tr2aacds.pl VERSION 2016.07.11 See http://eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Snapshots: No snapshots

Created: 10th Nov 2019 at 22:39, Last updated: 13th Nov 2019 at 22:34

_A__S_01_sequences-files

_p_stRT

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Andrej Blejec

NGS sequences for de novo assembly NGS sequences for de novo assembly; input for Study 02_denovo

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_STRT-1

Study: _S_01_sequences

Organisms: No organisms

SOPs: No SOPs

Data files: /reports/SupplementaryTableS1-Input_sequences_i..., /reports/SupplementaryTableS1-Input_sequences_i...

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:04, Last updated: 13th Nov 2019 at 22:25

_A__S_02_denovo-files

_p_stRT

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Andrej Blejec

De novo assemblies De novo assemblies for cration of potato reference transcriptomes

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_STRT-1

Study: _S_02_denovo

Organisms: No organisms

SOPs: No SOPs

Data files: /reports/SupplementaryTableS2-Primary_potato_tr..., /reports/SupplementaryTableS2-Primary_potato_tr...

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:04, Last updated: 13th Nov 2019 at 22:25

_A__S_03_stCuSTr-files

_p_stRT

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Andrej Blejec

Solanum tuberosum Cultivar-Specific Transcriptomes Solanum tuberosum Cultivar-Specific Transcriptomes

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:05, Last updated: 13th Nov 2019 at 22:25

_A_02.1_BUSCO

_p_stRT

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Andrej Blejec

BUSCO on assemblies and tr2aacds output BUSCO on assemblies and tr2aacds output

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /input/path_to_files.txt, /output/Desiree_assemblies.txt, /output/Desiree_assemblies.txt, /output/Desiree_repAlt.txt, /output/Desiree_repAlt.txt, /output/PW363_assemblies.txt, /output/PW363_assemblies.txt, /output/PW363_repAlt.txt, /output/PW363_repAlt.txt, /output/Rywal_assemblies.txt, /output/Rywal_rep.aa.txt, /output/Rywal_rep.aa.txt, /output/Rywal_rep.tr.txt, /output/Rywal_rep.tr.txt, /output/Rywal_repAlt.txt, /output/Rywal_repAlt.txt, /scripts/00_get_tools_and_export_paths.txt, /scripts/00_get_tools_and_export_paths.txt, /scripts/01_run_BUSCO.sh, /scripts/01_run_BUSCO.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:06, Last updated: 19th Aug 2021 at 07:43

_A_02.2_assembly-contribution-count

_p_stRT

All creators

Andrej Blejec

assembly contribution count assembly contribution count, input/output tr2aacds

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:06, Last updated: 10th Nov 2019 at 23:06

_A_02.2_assembly-contribution-count

_p_stRT

All creators

Andrej Blejec

assembly contribution count assembly contribution count, input/output tr2aacds

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /input/path_to_files.txt, /intermediate_Desiree.tar.gz, /intermediate_Desiree.tar.gz, /intermediate_PW363.tar.gz, /intermediate_PW363.tar.gz, /intermediate_Rywal.tar.gz, /intermediate_Rywal.tar.gz, /output/Desiree_cnt_assemblies.txt, /output/Desiree_cnt_assemblies.txt, /output/PW363_cnt_assemblies.txt, /output/PW363_cnt_assemblies.txt, /output/Rywal_cnt_assemblies.txt, /output/Rywal_cnt_assemblies.txt, /scripts/countDesiree.sh, /scripts/countDesiree.sh, /scripts/countPW363.sh, /scripts/countPW363.sh, /scripts/countRywal.sh, /scripts/countRywal.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:06, Last updated: 13th Nov 2019 at 22:28

_A_02.3_InterProScan

_p_stRT

All creators

Andrej Blejec

InterProScan on tr2aacds output InterProScan on tr2aacds output

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:07, Last updated: 13th Nov 2019 at 22:29

_A_02.5_STARlong_matchAnnot

_p_stRT

All creators

Andrej Blejec

potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

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

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:08, Last updated: 13th Nov 2019 at 22:30

_A_02.6_TransRate

_p_stRT

All creators

Andrej Blejec

TransRate stat on raw tr2aacds transcriptomes TransRate stat on raw tr2aacds transcriptomes, basic and reference-based

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:08, Last updated: 13th Nov 2019 at 22:30

_A_02.7_VecScreen

_p_stRT

All creators

Andrej Blejec

VecScreen on raw tr2aacds output VecScreen and blastn on raw tr2aacds output

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

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: No snapshots

Created: 10th Nov 2019 at 23:09, Last updated: 10th Nov 2019 at 23:09

_A_03.1_filtering

_p_stRT

All creators

Andrej Blejec

Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate/intermediate-2-validate-removal.t..., /output/Desiree_tr.cds.tsv.gz, /output/PW363_tr.cds.tsv.gz, /output/Rywal_tr.cds.tsv.gz, /reports/03.1_Rywal_combo_withFiltering.html, /reports/03.2_PW363_combo_withFiltering.html, /reports/03.3_Desiree_combo_withFiltering.html, /scripts/01_ID_length_pairs.sh, /scripts/02_get_otherFiles.sh, /scripts/03.1_Rywal_combo_withFiltering.Rmd, /scripts/03.2_PW363_combo_withFiltering.Rmd, /scripts/03.3_Desiree_combo_withFiltering.Rmd, /scripts/04_summary.sh, /scripts/05_validate_removal.sh, /scripts/06_archive_files.sh