Assays

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59 Assays visible to you, out of a total of 59

_A_02.1_BUSCO

_p_stRT

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_09_annotation-GFFmerged

_p_stRT

Short Name: 09_annotation-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: Pan-transcriptome fasta files annotation Description: Annotation of pan-transcriptome and re-annotation of cultivar-specific transcriptomes pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /output/annot_stCuSTr-D_aa_alternatives.zip, /output/annot_stCuSTr-D_cds_all.zip, /output/annot_stCuSTr-D_tr_all.zip, /output/annot_stCuSTr-P_aa_all.zip, /output/annot_stCuSTr-P_cds_all.zip, /output/annot_stCuSTr-P_tr_all.zip, /output/annot_stPanTr.aa.zip, /output/annot_stPanTr_alt.aa.zip, /scripts/annotate.sh

Snapshots: No snapshots

Created: 13th May 2021 at 11:56, Last updated: 13th May 2021 at 17:31

_A_08_centrifuge_3cvs-GFFmerged

_p_stRT

Short Name: 08_centrifuge_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: Centrigufe pan-transcriptome sequence classification Description: Classify cv rep transcripts and pan-transcriptome singletons based on taxonomy pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /intermediate/trueSingle.DM.cds.fasta, /intermediate/trueSingle.polyploid.cds.fasta, /intermediate/trueSingle.polyploid.tr.fasta, /output/PW363_report.txt, /output/trueSingle.polyploid.tr_kreport.txt

Snapshots: No snapshots

Created: 13th May 2021 at 17:28, Last updated: 13th May 2021 at 17:31

_A_07_Desiree-mapping

_p_stRT

Short Name: 07_Desiree-mapping Assay Class: DRY Assay Type: mapping Title: Desiree mapping Description: Mapping of Desiree samples (drought stress) to Desiree and Phureja transcriptomes pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /intermediate/Desiree/genomeParameters.txt, /intermediate/PGSC/chrName.txt, /intermediate/PGSC/chrNameLength.txt, /intermediate/gff-merged/chrName.txt, /intermediate/indexGFFmerged.log, /output/Desiree_SRR10416847/Log.final.out, /output/Desiree_SRR10416848/Log.final.out, /output/Desiree_SRR10416849/Log.progress.out, /output/Desiree_SRR10416849/Log.progress.out, /output/Desiree_drought123/Log.out, /output/PGSC_SRR10416848/Log.final.out, /output/PGSC_SRR10416849/Log.out, /output/PGSC_drought123/Log.out, /output/PGSC_drought123/Log.progress.out, /output/gff-merged_SRR10416847/Log.out, /output/gff-merged_SRR10416847/Log.progress.out, /output/gff-merged_SRR10416849/Log.final.out

Snapshots: No snapshots

Created: 13th May 2021 at 11:56, Last updated: 13th May 2021 at 17:31

_A_06_tr_rep-transrate

_p_stRT

Short Name: 06_tr_rep-transrate Assay Class: DRY Assay Type: transrate Title: Cultivar representative transcriptome transrate Description: Transrate on cultivar specific representatives, GFF merged as a reference for CRRB pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /output/PGSC_DM_v3.4_transcript-update_represen..., /output/PGSC_DM_v3.4_transcript-update_represen..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_...

Snapshots: No snapshots

Created: 13th May 2021 at 11:38, Last updated: 13th May 2021 at 17:28

_A_01_evigene

_p_stRT

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_04-MSA

_p_stRT

Short Name: 04-MSA Assay Class: DRY Assay Type: MSA Title: Multiple sequence alignment, pantranscriptomes' paralogue clusters Description: Multiple sequence alignment, pantranscriptomes' paralogue clusters 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_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /output/5cv_weak-components.txt, /output/out_aa_ClustalOmega_selected_4_wc_150_o..., /output/out_aa_ClustalOmega_selected_4_wc_150_o..., /output/out_aa_ClustalOmega_selected_4_wc_150_o..., /output/out_aa_ClustalOmega_selected_4_wc_150_o..., /output/out_aa_ClustalOmega_selected_4_wc_150_o..., /output/out_cds_ClustalOmega_selected_4_wc_150_...

Snapshots: No snapshots

Created: 15th Nov 2019 at 00:23, Last updated: 15th Nov 2019 at 00:26

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