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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
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Created: 15th Nov 2019 at 00:20
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Projects: testUpload, Test project 2019-10-30 11:13:00, Test project 2019-10-30 11:09:39, Test project 2019-11-02 19:40:30, Test project for pISA (104), _p_stRT, _p_Demo, Bla, Test project abcd, Test project 2021-07-18 22:00:39, Test project 2021-07-18 22:45:54, Test project 2021-07-18 23:08:33, Test project 2021-07-18 23:23:02, Test project 2021-07-21 00:08:04, Test project 2021-07-21 00:17:06, Test project 2021-07-21 00:18:25, Test project 2021-08-20 22:56:43, Testing of upload, _p_RNAinVAL
Institutions: National Institute of Biology, NIB, <script>alert('xss-institution-title')</script> & Test Institution
https://orcid.org/0000-0001-7484-6031Expertise: STatistics, R, Programming, Data Management
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
Snapshots: No snapshots
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: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /bla.r, /bla.r, /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
Snapshots: No snapshots
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: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /scripts/01_potato_tr_evigene_IPS_commands.txt
Snapshots: No snapshots
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: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /output/fasta_1B_alt-per-cv/stCuSTr-P_tr_altern..., /scripts/i1.2_parse-fasta-files-pt2.pl, /scripts/i1.3_parse-headers.pl, /scripts/i5.1_parse-cdhit-2d.sh, /scripts/i5.3_prepare-fastas.sh
Snapshots: No snapshots
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: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
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: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /output/Desiree.cds_SP_TrEMBL_plants.out.ENCHfo..., /output/Desiree.cds_solanumTuberosum.out.ENCHfo..., /output/PW363.tr_SwissProt_TrEMBL.out.ENCHforma..., /scripts/03_archive_files.sh
Snapshots: No snapshots
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: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /output/PW363_tr.cds.tsv.gz, /scripts/04_summary.sh, /scripts/06_archive_files.sh
Snapshots: No snapshots
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: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
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: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
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: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /output/Rywal_rep.tr.txt
Snapshots: No snapshots
Change license MIT-ni id
Creator: Andrej Blejec
Submitter: Andrej Blejec
Data file assoc with assay
Creator: Andrej Blejec
Submitter: Andrej Blejec
Testing of upload
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_03.1_filtering
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.2_components
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_03_stCuSTr/_A_02.3_InterProScan
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.2_components
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_03_stCuSTr/_A_02.8_DIAMOND
Creator: Andrej Blejec
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_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering
Creator: Andrej Blejec
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_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.2_components
Creator: Andrej Blejec
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_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.8_DIAMOND
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.2_components
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.2_components
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
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_p_stRT/_I_STRT/_S_03_stCuSTr/_A_01_evigene
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_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