_S_03_stCuSTr

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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

SEEK ID: https://testing.sysmo-db.org/studies/147

Investigation: _I_STRT

Projects: _p_stRT

Study position:

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Creators and Submitter

Creator

Andrej Blejec

Submitter

Andrej Blejec

Activity

Views: 652

Created: 15th Nov 2019 at 00:20

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (9)
Data files (21)
Documents (12)

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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

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_p_stRT

Test project for upload

Programme: pISA-tree

Public web page: Not specified

Organisms: Not specified

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_I_STRT

_p_stRT

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Andrej Blejec

No description 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

Created: 14th Nov 2019 at 12:22

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_A_01_evigene

_p_stRT

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Andrej Blejec

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

Created: 15th Nov 2019 at 00:20, Last updated: 20th Nov 2019 at 16:28

_A_02.3_InterProScan

_p_stRT

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Andrej Blejec

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

Created: 15th Nov 2019 at 00:22, Last updated: 15th Nov 2019 at 00:24

_A_03.2_components

_p_stRT

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Andrej Blejec

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

Created: 15th Nov 2019 at 00:22, Last updated: 15th Nov 2019 at 00:25

_A_02.2_assembly-contribution-count

_p_stRT

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Andrej Blejec

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

Created: 15th Nov 2019 at 00:23, Last updated: 15th Nov 2019 at 00:23

_A_02.8_DIAMOND

_p_stRT

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Andrej Blejec

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

Created: 15th Nov 2019 at 00:23, Last updated: 15th Nov 2019 at 00:25

_A_03.1_filtering

_p_stRT

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Andrej Blejec

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

Created: 15th Nov 2019 at 00:23, Last updated: 15th Nov 2019 at 00:25

_A_02.4_STAR

_p_stRT

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Andrej Blejec

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

Created: 15th Nov 2019 at 00:23, Last updated: 15th Nov 2019 at 00:23

_A_05_BUSCO

_p_stRT

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Andrej Blejec

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

Created: 15th Nov 2019 at 00:25, Last updated: 15th Nov 2019 at 00:25

_A_02.1_BUSCO

_p_stRT

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Andrej Blejec

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

Created: 15th Nov 2019 at 00:26

Showing 20 out of a possible 21 Data files Advanced Data files list for this Study with search and filtering

/output/Rywal_rep.tr.txt

_p_stRT

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Andrej Blejec

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