Maja Zagorscak
Computational Biologist, Young Researcher at Department of Biotechnology and Systems Biology, National Institute of Biology NIB and PhD candidate in Statistics, Ljubljana, Slovenia
SEEK ID: https://fairdomhub.org/people/1098
Location:
Slovenia
Expertise: computational biology, Molecular Biology, Statistics, Bioinformatics, Mathematical and statistical modeling, Programming, Data analysisMathematical modellingBioinformaticsSystems biology, Data Management, Data analysis, Data integration, Visualization
Tools: Bioinformatics, Computational and theoretical biology, Computational Systems Biology, Data integration, Data Management, Databases, Dynamic modelling, Molecular Biology, Python, R, Systems Biology
https://orcid.org/0000-0002-1669-6482 
Project roles
Project administrator
Asset housekeeper
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Their tagsRelated 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,
...
Programme: NIBSys
Public web page: http://www.nib.si/eng/index.php/systems-biology
Start date: 1st Dec 2017
End date: 1st Jan 2020
Our world is changing fast! Key global trends are rapid urbanisation, growing and ageing populations, and increased prosperity. This results in depletion of natural and petrochemical resources and climate change, which affects the quality of the environment and people's lives. Therefore, developing a bio-based economy is key to sustain our planet in the long term. Raw materials will have to be recruited from renewable sources.
Industrial biotechnology is potentially a very powerful technology in
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Programme: NIBSys
Public web page: https://indie.cebitec.uni-bielefeld.de/
pISA-tree: Standard project directory tree (ISA compliant)
Development of support for standardization of directory trees to suport ISA framework of research organization. We are developing a set of batch/make files to enable creation of trees for storage of assets (data/presentations/protocols/scripts) and description files that hold associated metadata for Investigation / Study / Assay levels.
Programme: NIBSys
Public web page: http://ablejec.nib.si/doc
Despite the intensive use of agrochemicals, plant pathogens are responsible for huge yield losses worldwide. Understanding the interaction between plant and pathogens is crucial to ensure long lasting and environmentally friendly system of plant protection. Therefore research of the most important human food crops in combination with their pathogens is one of the highest priorities for sustainable agriculture.
The aim of the proposed research project is to bring new perspective into understanding
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Programme: NIBSys
Public web page: http://projects.nib.si/hyp/
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
Supplementary Information linked together
Person responsible: Maja Zagorscak
Snapshots: No snapshots
Study: _S_03_stCuSTr
Short Name: 03_stCuSTr
Title: Solanum tuberosum Cultivar-Specific Transcriptomes
Description: Solanum tuberosum Cultivar-Specific Transcriptomes
Raw Data: ../_S_01_sequences/, ../_S_02_denovo/
pISA Study creation date: 2019-10-22
pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes
RELATED FILES:
/reports/README.MD https://fairdomhub.org/documents/346
/_STUDY_METADATA.TXT
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Person responsible: Maja Zagorscak
Snapshots: No snapshots
Study: _S_02_denovo
Short Name: 02_denovo
Title: De novo assemblies
Description: De novo assemblies for cration of potato reference transcriptomes
Raw Data: ../_S_01_sequences/
pISA Study creation date: 2019-10-23
pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes
RELATED FILES:
/reports/README.MD https://fairdomhub.org/documents/343
/_STUDY_METADATA.TXT https://fairdomhub.org/documents/342
...
Study: _S_01_sequences
Short Name: 01_sequences
Title: NGS sequences for de novo assembly
Description: NGS sequences for de novo assembly; input for Study 02_denovo
Raw Data: see: ./reports/SupplementaryTableS1-Input_sequences_information.xlsx
pISA Study creation date: 2019-10-23
pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes
RELATED FILES:
/reports/README.MD
...
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:
Supplementary Information linked together
Contributor: Maja Zagorscak
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
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:
Contributor: Andrej Blejec
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
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:
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:
Contributor: Andrej Blejec
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
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:
Contributor: Andrej Blejec
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
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:
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:
Contributor: Andrej Blejec
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
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:
Contributor: Andrej Blejec
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
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
Contributor: Andrej Blejec
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Assay: _A_03.1_filtering
Short Name: 03.1_filtering
Assay Class: DRY
Assay Type: filtering
Title: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
Description: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
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
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
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
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
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
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
...
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
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
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
DownloadSupplementary Table S1 - Detailed sample information table used to generate the de novo transcriptome assemblies.
Raw and processed reads summary.
Layer _p_stRT/_I_STRT/ _S_01_sequences/reports
Creators: Maja Zagorscak, Marko Petek
Contributor: Maja Zagorscak
Supplementary Table S2 - Detailed de novo assemblies information table.
Primary potato transcriptome assemblies summary listing parameters used for short-read de novo assembly generation.
Layer _p_stRT/_I_STRT/_S_02_denovo/reports/
Creators: Maja Zagorscak, Marko Petek
Contributor: Maja Zagorscak
Number of transcripts from de novo assemblies contributing to cultivar Désirée, transcriptome and number of complete BUSCOs found in assemblies.
Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown.
Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet.
Supplementary Table S8 - Read count summary for Désirée drought samples mapped to the representative Phureja DM and Désirée reference transcriptomes.
Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_07_Desiree-mapping/reports/
Supplementary Table S7 - Paralogue cluster information for cultivar-specific and pantranscriptome sequences extended with annotations and quality classification.
Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged/reports/
Supplementary File 1 - Merged ITAG/PGSC Phureja DM gene models.
Archive containing GTF, CDS and peptide fasta files for merged ITAG and PGSC gene models for S. tuberosum Group Phureja DM genome v4.04
Supplementary Table S6 - EvidentialGene Summary Statistics for PacBio sequences.
Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.2_assembly-contribution-count/reports/
Supplementary Table S5 - Rywal biological evidence filtering results.
Output of 1st filtering step by biological evidence for cv. Rywal.
Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/
Supplementary Table S4 - PW363 biological evidence filtering results.
Output of 1st filtering step by biological evidence for breeding clone PW363.
Layer _p_stRT/ _I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/,
Supplementary Table S3 - Désirée biological evidence filtering results.
Output of 1st filtering step by biological evidence for cv. Désirée.
Layer _p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering/reports/
Supplementary Figure 3 - Venn diagrams showing the overlap of paralogue clusters in cultivar-specific transcriptomes and merged Phureja DM gene model.
Representatives and alternatives of the stPanTr (pan-transcriptome) paralogue cluster are counted as well as alternatives defined at stCuSTr (cultivar-specific transcriptome) step. For Phureja, the merged ITAG and PGSC DM gene models were counted.
Layer _p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged/reports/
Number of transcripts from de novo assemblies contributing to breeding clone PW363, transcriptome and number of complete BUSCOs found in assemblies.
Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet, Sdn - SPAdes.
Number of transcripts from de novo assemblies contributing to cultivar Rywal, transcriptome and number of complete BUSCOs found in assemblies.
Proportion of all contigs in de novo assembly (blue bars) and proportion of EvidentialGene okay set (green bars), and the number of complete BUSCOs (dots) using https://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz set are shown. Assembly software abbreviations: CLCdn - CLC Genomics Workbench, Vdn - Velvet, Sdn - SPAdes, PBdn - PacBio.
Abstract (Expand)
Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden
Date Published: No date defined
Publication Type: Not specified
Description of Tags found on transcript headers
https://ncgas.org/Blog_Posts/EviGene.php#step3
Creator: Sheri Sanders
Contributor: Maja Zagorscak
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_01_sequences
Creators: Maja Zagorscak, Marko Petek
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_01_sequences
Creators: Maja Zagorscak, Marko Petek
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_02_denovo
Creators: Maja Zagorscak, Marko Petek
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_02_denovo
Creators: Maja Zagorscak, Marko Petek
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_03_stCuSTr
Creators: Maja Zagorscak, Ziva Ramsak
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_03_stCuSTr
Creators: Maja Zagorscak, Ziva Ramsak
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr
Creators: Maja Zagorscak, Ziva Ramsak
Contributor: Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr
Creators: Maja Zagorscak, Ziva Ramsak
Contributor: Maja Zagorscak
pISA-tree: Standard project directory tree (ISA-tab compliant) - NIB-SI/pISA
https://github.com/NIB-SI/pISA/
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Contributor: Maja Zagorscak
Creator: Maja Zagorscak
Contributor: Maja Zagorscak
Creator: Maja Zagorscak
Contributor: Maja Zagorscak
