_p_stRT
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OverviewTest project for upload
Programme: pISA-tree
SEEK ID: https://testing.sysmo-db.org/projects/105
Public web page: Not specified
Organisms: No Organisms specified
FAIRDOM PALs: No PALs for this Project
Project created: 6th Nov 2019
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Institutions: National Institute of Biology, NIB, <script>alert('xss-institution-title')</script> & Test Institution
https://orcid.org/0000-0001-7484-6031
Local data management; testing uploading/downloading using API
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Web page: Not specified
Submitter: Andrej Blejec
Studies: /output/Desiree_SRR10416847/Log.final.out, _S_03_stCuSTr, _S_04_stPanTr
Assays: _A_01_evigene, _A_01_evigene_1_3cvs-gffmerged, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _A_02.3_InterProScan, _A_02.4_STAR, _A_02.8_DIAMOND, _A_03.1_filtering, _A_03.2_components, _A_04-MSA, _A_05_BUSCO, _A_05_BUSCO-Stat, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Studies: _S_01_sequences, _S_01_sequences, _S_01_sequences, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr, _S_03_stCuSTr
Assays: _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_01_evigene, _A_02.8_DIAMOND, _A__S_01_sequences-files, _A__S_01_sequences-files, _A__S_01_sequences-files, _A__S_01_sequences-files
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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
Submitter: Andrej Blejec
Studies: _S_01_sequences, _S_02_denovo, _S_03_stCuSTr, _S_04_stPanTr
Assays: _A_01_evigene, _A_01_evigene_1_3cvs-gffmerged, _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_02_components_1_3cvs-gffmerged, _A_03.1_filtering, _A_03.2_components, _A_03_BUSCO_1_3cvs-gffmerged, _A_04-MSA, _A_04_TransRate, _A_05_BUSCO, _A_05_BUSCO-Stat, _A_05_BUSCO-Stat-old, _A__S_01_sequences-files, _A__S_02_denovo-files, _A__S_03_stCuSTr-files, _A__S_04_stPanTr-files
_p_stRT/_I_STRT/_S_04_stPanTr/_A_07_Desiree-mapping
Short Name: 04_stPanTr Title: Solanum tuberosum Pan-Transcriptome Description: Solanum tuberosum Pan-Transcriptome Raw Data: _S_03_stCuSTr/ pISA Study creation date: 2019-10-22 pISA Study creator: Maja Zagorscak Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Investigation: _I_STRT
Assays: _A_01_evigene_1_3cvs-gffmerged, _A_04-MSA, _A_05_BUSCO-Stat, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
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_02.8_DIAMOND, _A_03.1_filtering, _A_03.2_components, _A_05_BUSCO
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_STRT-1
Study: _S_03_stCuSTr
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_STRT-1
Study: _S_03_stCuSTr
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
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
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
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
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
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
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
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
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
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
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
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
Components: tr2aacds headers, cdhit-2d Components: tr2aacds headers, cdhit-2d; postfiltering redefinition of paralogue clusters
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT-1
Study: _S_03_stCuSTr
TransRate post filtering and reassignment TransRate post filtering and reassignment
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT-1
Study: _S_03_stCuSTr
BUSCO post filtering and reassignment BUSCO post filtering and reassignment
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT-1
Study: _S_03_stCuSTr
Solanum tuberosum Pan-Transcriptome Solanum tuberosum Pan-Transcriptome
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_STRT-1
Study: _S_04_stPanTr
tr2aacds on cv rep and gffmerged tr2aacds on cv rep and gffmerged
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT-1
Study: _S_04_stPanTr
paralogue clusters on pantranscriptome paralogue clusters on pantranscriptome
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT-1
Study: _S_04_stPanTr
Creator: Andrej Blejec
Submitter: Andrej Blejec
DownloadCreator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
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Submitter: Andrej Blejec
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Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.8_DIAMOND
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_04_stPanTr/_A_05_BUSCO-Stat
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_05_BUSCO
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.4_STAR
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.2_assembly-contribution-count
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.3_InterProScan
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_01_evigene
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_01_evigene
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_01_evigene
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_01_evigene
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_01_evigene
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_01_evigene
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_01_evigene
Creator: Andrej Blejec
Submitter: Andrej Blejec
