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Created: 22nd Mar 2020 at 00:11
Last updated: 22nd Mar 2020 at 00:11
Last used: 20th Jan 2021 at 07:22

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Related items
project: _p_stRT
Short Name: stRT
Title: Solanum tuberosum Reference Transcriptomes
Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
pISA projects path: ../pISA-Projects
Local pISA-tree organisation: National Institute of Biology
pISA project creation date: 2019-10-22
pISA project creator: Maja Zagorscak, Ziva Ramsak, Marko Petek
Project funding code: This project was supported by the Slovenian Research Agency (grants P4-0165, J4-4165, J4-7636,
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Programme: NIBSys
Public web page: http://www.nib.si/eng/index.php/systems-biology
Start date: 1st Dec 2017
End date: 1st Jan 2020
Organisms: Solanum tuberosum, Potato virus Y
Investigation: _I_STRT
Short Name: STRT
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, Ziva Ramsak, Marko Petek
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes
RELATED
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Snapshots: No snapshots
Studies: SupplementaryInformation, _S_01_sequences, _S_02_denovo, _S_03_stCuSTr, _S_04_stPanTr
Assays: Supplementary Information, _A_01_GC_content-count, _A_01_evigene, _A_02.1_BUSCO, _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_cdhit_3cvs-GFFmerged, _A_03.1_filtering, _A_03.2_components, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_04_TransRate, _A_05_BUSCO, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
Short Name: 04_stPanTr
Title: Solanum tuberosum Pan-Transcriptome
Description: Solanum tuberosum Pan-Transcriptome
Raw Data:
pISA Study creation date: 2019-10-22
pISA Study creator: Maja Zagorscak
Principal investigator: Kristina Gruden
License: CC BY 4.0
Sharing permission: Public
Upload to FAIRDOMHub: Yes
Person responsible: Andrej Blejec
Snapshots: No snapshots
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:
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /input/taxdmp.tgz, /input/trueSingle.DM.ID, /input/trueSingle.polyploid.ID, /intermediate/trueSingle.DM.cds.fasta, /intermediate/trueSingle.polyploid.cds.fasta, /intermediate/trueSingle.polyploid.tr.fasta, /output/Desiree_centrifuge.txt, /output/Desiree_kreport.txt, /output/Desiree_report.txt, /output/PW363_centrifuge.txt, /output/PW363_kreport.txt, /output/PW363_report.txt, /output/Rywal_centrifuge.txt, /output/Rywal_kreport.txt, /output/Rywal_report.txt, /output/Tetraploid_transcriptomes-report.html, /output/Uploaded_sample_set-report.html, /output/pavian_class_summary_No.csv, /output/pavian_class_summary_perc.csv, /output/sankey-Desiree.html, /output/sankey-PW363.html, /output/sankey-Rywal.html, /output/sankey-trueSingle.DM.cds.html, /output/sankey-trueSingle.polyploid.cds.html, /output/sankey-trueSingle.polyploid.tr.html, /output/trueSingle.DM.cds_centrifuge.txt, /output/trueSingle.DM.cds_kreport.txt, /output/trueSingle.DM.cds_report.txt, /output/trueSingle.polyploid.cds_centrifuge.txt, /output/trueSingle.polyploid.cds_kreport.txt, /output/trueSingle.polyploid.cds_report.txt, /output/trueSingle.polyploid.tr_centrifuge.txt, /output/trueSingle.polyploid.tr_kreport.txt, /output/trueSingle.polyploid.tr_report.txt, /reports/SupplementaryFile3.html, /scripts/01_prepareFasta.sh, /scripts/02_centrifuge_commands.txt