Assays

23 Assays visible to you, out of a total of 23

_p_stRT

Assay: _A_02.4_STAR 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: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/samtoolsCoverage.zip, /reports/summaryCounts&SJ.xlsx, /scripts/STAR_commands.txt

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1165.1

Created: 7th Nov 2019 at 16:48, Last updated: 2nd Jun 2020 at 13:42

_A_02.2_assembly-contribution-count

_p_stRT

Assay: _A_02.2_assembly-contribution-count 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: Maja Zagorscak

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_Desiree.tar.gz, /intermediate_PW363.tar.gz, /intermediate_Rywal.tar.gz, /output/output.tar, /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /reports/SupplementaryFigure3.pdf, /reports/SupplementaryTableS6, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1163.1

Created: 7th Nov 2019 at 16:04, Last updated: 26th Feb 2020 at 13:00

_A_01_evigene

_p_stRT

Assay: _A_01_evigene 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: Maja Zagorscak

Biological problem addressed: Integration

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /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, /output/output.tar, /scripts/01_run_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh

Snapshots: Snapshot 1

Created: 7th Nov 2019 at 15:54, Last updated: 16th Nov 2019 at 13:21

_A_02.1_BUSCO

_p_stRT

Assay: _A_02.1_BUSCO 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: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1162.1

Created: 7th Nov 2019 at 15:57, Last updated: 16th Nov 2019 at 12:40

_A_02.3_InterProScan

_p_stRT

Assay: _A_02.3_InterProScan 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: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate/intermediate.tar, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1164.1

Created: 7th Nov 2019 at 16:46, Last updated: 16th Nov 2019 at 12:35

_A_02.5_STARlong_matchAnnot

_p_stRT

Assay: _A_02.5_STARlong_matchAnnot Short Name: 02.5_STARlong_matchAnnot Assay Class: DRY Assay Type: matchAnnot Title: potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations Description: potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None ...

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_1_STARlong-logs-n-SJ.tar.gz, /output/output_2_matchAnnot-parsed-txt.tar.gz, /scripts/STARlongMatchAnnot_commands_ENCODE_den...

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1166.1

Created: 7th Nov 2019 at 16:50, Last updated: 16th Nov 2019 at 11:55

_A_02.6_TransRate

_p_stRT

Assay: _A_02.6_TransRate Short Name: 02.6_TransRate Assay Class: DRY Assay Type: TransRate Title: TransRate stat on raw tr2aacds transcriptomes Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Nonde Data: see ./input/path_to_files.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1167.1

Created: 7th Nov 2019 at 16:54, Last updated: 16th Nov 2019 at 11:45

_A_02.7_VecScreen

_p_stRT

Assay: _A_02.7_VecScreen Short Name: 02.7_VecScreen Assay Class: DRY Assay Type: VecScreen Title: VecScreen on raw tr2aacds output Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) 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: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate.tar.gz, /output/Desiree_vecscreen.tsv, /output/PW363_vecscreen.tsv, /output/Rywal_vecscreen.tsv, /scripts/01_get_input.sh, /scripts/02_VecScreenPlus_blastn.sh, /scripts/ENCH_sumablastplus.pl

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1168.1

Created: 7th Nov 2019 at 16:58, Last updated: 16th Nov 2019 at 11:37

_A_02.8_DIAMOND

_p_stRT

Assay: _A_02.8_DIAMOND 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: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1169.1

Created: 7th Nov 2019 at 17:02, Last updated: 16th Nov 2019 at 11:28

_A_04_TransRate

_p_stRT

Assay: _A_04_TransRate Short Name: 04_TransRate Assay Class: DRY Assay Type: TransRate Title: TransRate post filtering and reassignment Description: TransRate 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: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output.tar, /scripts/run_TransRate_commands.sh

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1172.1

Created: 7th Nov 2019 at 17:09, Last updated: 16th Nov 2019 at 11:22

_A_05_BUSCO

_p_stRT

Assay: _A_05_BUSCO 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: Maja Zagorscak

Biological problem addressed: Validation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar, /transfer/transfer.zip

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1173.1

Created: 7th Nov 2019 at 17:11, Last updated: 16th Nov 2019 at 11:08

_A_03.2_components

_p_stRT

Assay: _A_03.2_components 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: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_4_cdhit-2d.tar.gz, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1171.1

Created: 7th Nov 2019 at 17:06, Last updated: 15th Nov 2019 at 20:07