Assays

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11 Assays visible to you, out of a total of 43

_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

Snapshots: No snapshots

Created: 19th Mar 2020 at 11:00, Last updated: 5th May 2022 at 23:38

_A_02_cdhit_3cvs-GFFmerged

_p_stRT

Short Name: cdhit_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC Description: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC pISA Assay creation date: 2020-03-09 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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.1263.2

Created: 18th Mar 2020 at 20:44, Last updated: 5th May 2022 at 23:36

_A_01_GC_content-count

_p_stRT

Short Name: 01_GC_content-count Assay Class: DRY Assay Type: count Title: GC content and sequence length Description: A, C, T, G content and sequence length pISA Assay creation date: 2020-03-09 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data: ../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: /input/Solanum_tuberosum-ITAG_DM_v1_cds.fasta, /input/Solanum_tuberosum_PGSC_merged.fasta, /input/StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_gf..., /output/Solanum_tuberosum-ITAG_DM_v1_cds_GC.txt, /output/Solanum_tuberosum_PGSC_merged.CDS_GC.txt, /output/StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_g..., /scripts/GC_content.py, /scripts/tab_to_fasta.py and 12 hidden items

Snapshots: No snapshots

Created: 19th Mar 2020 at 10:02, Last updated: 5th May 2022 at 23:34

General

pISA-tree

General sandbox

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

Study: FAIRDOMhub API usage in R

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: Test API connection to FAIRDOMHub, Test API connection to FAIRDOMHub, dummy file

Snapshots: No snapshots

Created: 11th Jun 2018 at 22:27, Last updated: 18th Aug 2021 at 23:39

_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

Snapshots: No snapshots

Created: 19th Mar 2020 at 10:38, Last updated: 12th Apr 2020 at 09:51

_A_05_MSA_3cvs-GFFmerged

_p_stRT

Short Name: 05_MSA_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: MSA 3cv and GFF-merged Description: Multiple sequence alignment of Desiree, PW363, Rywal and ITAG/PGSC pISA Assay creation date: 2020-03-10 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: /input/folderWithIds/test.IDs1, /input/folderWithIds/test.IDs2, /input/my.test.aa.fasta, /input/path_to_files.txt, /reports/SupplementaryFile2.html, /scripts/MSA-commands.txt, /scripts/MSA.py, /scripts/print.sh

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.1270.2

Created: 19th Mar 2020 at 10:58, Last updated: 12th Apr 2020 at 09:42

_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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.1268.2

Created: 19th Mar 2020 at 10:41, Last updated: 9th Apr 2020 at 10:14

_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

Snapshots: No snapshots

Created: 22nd Mar 2020 at 23:09, Last updated: 6th Apr 2020 at 23:50

_A_03_components_3cvs-GFFmerged

_p_stRT

Short Name: 03_components_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: components Description: representative and alternative pan-transcriptome CDS and polypeptide fasta files pISA Assay creation date: 2020-03-10 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: /input/path_to_files.txt, /output/Solanum_tuberosum_PGSC_DM_v4.04_CDS-to-..., /output/alt.aa.IDs, /output/alt.cds.IDs, /output/rep.aa.IDs, /output/rep.cds.IDs, /scripts/commands-components_1_3cvs-gffmerged.txt

Snapshots: No snapshots

Created: 19th Mar 2020 at 10:55, Last updated: 6th Apr 2020 at 23:48

_A_04_BUSCO_3cvs-GFFmerged

_p_stRT

Short Name: 04_BUSCO_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: BUSCOs Description: BUSCO on ITAG, PGSC, ITAG/PGSC merged, pan-transcriptome representatives, pan-transcriptome alternatives, and pan-transcriptome pISA Assay creation date: 2020-03-10 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

Snapshots: No snapshots

Created: 19th Mar 2020 at 10:13, Last updated: 6th Apr 2020 at 23:46

_A_99_Empty

pISA-tree

Empty assay

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

Study: FAIRDOMhub API usage in R

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: No Data files

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1190.1

Created: 19th Nov 2019 at 10:37, Last updated: 20th Nov 2019 at 10:32

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