_S_04_stPanTr

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

SEEK ID: https://testing.sysmo-db.org/studies/124

Investigation: _I_STRT-1

Projects: _p_stRT

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Creators and Submitter

Creator

Andrej Blejec

Submitter

Andrej Blejec

Activity

Views: 947

Created: 10th Nov 2019 at 23:16

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (7)
Data files (115)
Documents (23)

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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-1

_p_stRT

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Andrej Blejec

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

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Created: 6th Nov 2019 at 22:25, Last updated: 13th Nov 2019 at 22:21

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_A__S_04_stPanTr-files

_p_stRT

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Andrej Blejec

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

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:16, Last updated: 10th Nov 2019 at 23:16

_A_01_evigene_1_3cvs-gffmerged

_p_stRT

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Andrej Blejec

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

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/StPGSC4.04n_PGSC-ITAG-merged_representat..., /input/StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_gf..., /input/path_to_files.txt, /output/2019-08-05_3cv_gffmerged_cds_tr2ac1_log..., /output/3cv_gffmerged_cds.tr2aacds.log.gz, /output/3cv_gffmerged_cds.trclass.gz, /output/3cv_gffmerged_cds.trclass.sum.txt.gz, /output/dropset/3cv_gffmerged_cds.drop.aa.gz, /output/dropset/3cv_gffmerged_cds.drop.cds.gz, /output/dropset/3cv_gffmerged_cds.drop.fasta.gz, /output/inputset/3cv_gffmerged_cds.aa.gz, /output/inputset/3cv_gffmerged_cds.aa.qual.gz, /output/inputset/3cv_gffmerged_cds.cds.gz, /output/okayset/3cv_gffmerged_cds.okalt.aa.gz, /output/okayset/3cv_gffmerged_cds.okalt.cds.gz, /output/okayset/3cv_gffmerged_cds.okalt.fasta.gz, /output/okayset/3cv_gffmerged_cds.okay.aa.gz, /output/okayset/3cv_gffmerged_cds.okay.cds.gz, /output/okayset/3cv_gffmerged_cds.okay.fasta.gz, /output/retrieve/diff.aa.IDs.txt.gz, /output/retrieve/diff.cds.IDs.txt.gz, /output/retrieve/diff.tr.IDs.txt.gz, /scripts/01_run_3cv_gffmerged_cds_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:16, Last updated: 10th Nov 2019 at 23:18

_A_02_components_1_3cvs-gffmerged

_p_stRT

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Andrej Blejec

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

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/3cvs_sequences_keep.txt.gz, /input/pantr_aa.fasta.gz, /input/pantr_cds.fasta.gz, /input/pantr_tr.fasta.gz, /input/phureja_sequences_keep.txt.gz, /output/stPanTr_aa_alternatives.fasta.gz, /output/stPanTr_aa_representatives.fasta.gz, /output/stPanTr_cds_alternatives.fasta.gz, /output/stPanTr_cds_representatives.fasta.gz, /output/stPanTr_tr_alternatives.fasta.gz, /output/stPanTr_tr_representatives.fasta.gz, /scripts/i1.0_copy-to-input.txt, /scripts/i1.2_parse-fasta-files-pt1.pl, /scripts/i1.2_parse-fasta-files-pt2.pl, /scripts/i1.3_parse-headers.pl, /scripts/i2.1_prepare-network.pl, /scripts/i2.3_parse-weak-components.pl, /scripts/i2.4_prepare-rep-component-table.pl, /scripts/i3.1_prepare-fastas-pt1.pl, /scripts/i4.1_compress-fastas.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:18, Last updated: 10th Nov 2019 at 23:19

_A_03_BUSCO_1_3cvs-gffmerged

_p_stRT

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Andrej Blejec

BUSCO on pantranscriptome BUSCO on pantranscriptome

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/BUSCO_stPanTr_embryophyta_odb9.tsv, /output/short_summary.tar, /scripts/run_BUSCO_commands.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:19, Last updated: 10th Nov 2019 at 23:19

_A_04-MSA

_p_stRT

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Andrej Blejec

Multiple sequence alignment, pantranscriptomes' paralogue clusters Multiple sequence alignment, pantranscriptomes' paralogue clusters

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:19, Last updated: 10th Nov 2019 at 23:23

_A_05_BUSCO-Stat-old

_p_stRT

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Andrej Blejec

BUSCO plots BUSCO plots

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate/BUSCO_stPanTr_embryophyta_odb9.tsv, /intermediate/BUSCOall_embryophyta_odb9.tsv, /intermediate/evg_out.tsv, /reports/BUSCO_plots.html, /scripts/BUSCO_plots.Rmd

Snapshots: No snapshots

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

_A_05_BUSCO-Stat

_p_stRT

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Andrej Blejec

Short Name: 05_BUSCO-Stat Assay Class: DRY Assay Type: Stat Title: BUSCO plots Description: BUSCO plots pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Analyst: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 13th Nov 2019 at 22:13

Showing 20 out of a possible 115 Data files Advanced Data files list for this Study with search and filtering

/scripts/BUSCO_plots.Rmd

_p_stRT

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Andrej Blejec

_p_stRT/_I_STRT/_S_04_stPanTr/_A_05_BUSCO-Stat