scripts/R_featureCounts_script.txt Version 1
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_CoExpNetViz/_A_02_Nb_datasets-CoExp/
SEEK ID: https://fairdomhub.org/data_files/5106?version=1
Filename:
scripts/R_featureCounts_script.txt
Format: Plain text document
Size: 1 KB
counts <- featureCounts(files, annot.inbuilt=FALSE, annot.ext="/DATA/mojcaj/STAR_mapping/NbAUSv1.0_AUGUSTUS-genes_2019-12-02.gff3", isGTFAnnotationFile=TRUE, GTF.featureType="gene", GTF.attrType="ID", GTF.attrType.extra=NULL, chrAliases=NULL, useMetaFeatures=FALSE, allowMultiOverlap=FALSE, minOverlap=1, fracOverlap=0, fracOverlapFeature=0, largestOverlap=FALSE, nonOverlap=NULL, nonOverlapFeature=NULL, readShiftType="upstream", readShiftSize=0, readExtension5=0, readExtension3=0, read2pos=NULL, countMultiMappingReads=TRUE, fraction=FALSE, isLongRead=FALSE, minMQS=0, splitOnly=FALSE, nonSplitOnly=FALSE, primaryOnly=FALSE, ignoreDup=FALSE, juncCounts=FALSE, genome=NULL, isPairedEnd=TRUE,bn requireBothEndsMapped=FALSE, checkFragLength=FALSE, minFragLength=40, maxFragLength=600, countChimericFragments=TRUE, autosort=TRUE, nthreads=16, byReadGroup=FALSE, reportReads=NULL, reportReadsPath=NULL, maxMOp=10, tmpDir=".", verbose=FALSE)
Export PNG
Creators and Submitter
Views: 1336 Downloads: 32
Created: 9th Apr 2022 at 20:15
Last updated: 21st Sep 2022 at 10:45
AttributionsNone
Version History
Version 1 (earliest) Created 9th Apr 2022 at 20:15 by Marko Petek
No revision comments
Related items
https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.
Synthetic biology data management spreadsheet: https://fairdomhub.org/data_files/6036
Programme: NIBSys
Public web page: http://susphire.info/susphireproject/
Start date: 1st Apr 2018
End date: 30th Sep 2021
Short Name: T21_SXPsysbio Title: Use a systems biology approach to identify regulatory bottlenecks in SxPv1 Description: Samples from SXPv1.0 plants as well as sister nulls (progeny from the original transgenic event in which the transgene has segregated) and wild type will be grown and leaf samples taken for RNA extraction and profiling of primary metabolites and volatiles (target pheromones as well as potential derivatives) (P1, P5). Phenotypic and GC-MS data will be obtained and analysed from ...
Submitter: Marko Petek
Studies: Investigation files, _S_P1_SPv10T0andT1, _S_P1_SPv10T2andT3, _S_P1_SPv1TransientExp, _S_P1_SxPAltAcTransferases, _S_P1_SxPv10vsSxP12, _S_P1_SxPv12T2, _S_P4_CoExpNetViz, _S_P4_DiNAR, _S_P4_GAtreat, _S_P4_SxP10-newG-DE, _S_P4_SxP10-oldG-DE, _S_P4_SxP1012-finalG, _S_P4_SxP12-newG-DE
Assays: _A_00_SxP_photos-phenotyping, _A_01_RNA1-RNAisol, _A_01_SxP_Data_Only-CoExp, _A_01_SxPv12_fastq-QC, _A_01_mapping-CLC, _A_01_toNewGenome-CLC-mapping, _A_02_FastQC-bioinfo, _A_02_Nb_datasets-CoExp, _A_02_SxPv12_mapping-CLC, _A_02_limmavoomDE-R, _A_02a_limmavoom-multim-R, _A_02a_limmavoomDEbylines-R, _A_02b_limmavoom-uniquem-R, _A_03_MapMan-visualisation, _A_03_NewGenome-MapMan, _A_03_SxPv12_limmavoom_DE-R, _A_03_mapping-CLC, _A_03a_mapping2-STAR, _A_04_GSEA-Stat, _A_04_MapManBINenrich-GSEA, _A_04_Mercator-bioinfo, _A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA, _A_05_DEstat-R, _A_05_Phenotype_analysis-Stat, _A_05_VOCcomp-Bioinfo, _A_05a_DEstat2-R, _A_05b_DElow-wt-R, _A_06_MapMan-bioinfo, _A_06_SxPv1-0_Illumina-Centrifuge, _A_07_NbAUSv1-0-InterPro, _A_07_transgenes-CLC, _A_CKN-DiNAR, _A_CKN_NbL35-DiNAR, _A_LeavesSxPv10vsv12-GCMS, _A_P4_v10v12-phenotyping, _A_PIS-DiNAR, _A_PIS-SxPv12-DiNAR, _A_PIS_NbL35-DiNAR, _A_RootsSxPv10vsv12-GCMS, _A_SP10T0Analysis-GCMS, _A_SP10T1Analysis-GCMS, _A_SPv10EaDActAnalysis-GCMS, _A_SPv10T2Analysis-GCMS, _A_SPv10T3Analysis-GCMS, _A_SPv10_phenotyping-Images, _A_SxPAlternativeAcetyltransferases-GCMS, _A_SxPv10vsv12-phenotyping, _A_SxPv12ScreeningT2-GCMS, _A_TransientSPv11andSPv12-GCMS, _I_T21_SXPsysbio-files, _S_P1_SPv10T0andT1-files, _S_P1_SPv10T2andT3-files, _S_P1_SPv1TransientExp-files, _S_P1_SxPAltAcTransferases-files, _S_P1_SxPv10vsSxP12-files, _S_P1_SxPv12T2-files, _S_P4_CoExpNetViz-files, _S_P4_DiNAR-files, _S_P4_GAtreat-files, _S_P4_SxP10-newG-DE-files, _S_P4_SxP10-oldG-DE-files, _S_P4_SxP1012-finalG-files, _S_P4_SxP12-newG-DE-files
Short Name: CoExpNetViz Title: CoExpNetViz Description: Coexpression analyses with CoExpNetViz tool. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_01_SxP_Data_Only-CoExp, _A_02_Nb_datasets-CoExp, _S_P4_CoExpNetViz-files
Short Name: 02_Nb_datasets-CoExp Assay Class: DRY Assay Type: CoExp Title: CoExp analysis using available Nb RNA-seq datasets Description: CoExpNetViz analysis using SUSPHIRE SxPv1.0 expression data together with available RNA-Seq datsets from Nicotiana benthamiana - average logCPM values or clculated logFCs were used as inputs to generate coexpression networks based on given baits. pISA Assay creation date: 2020-07-03 pISA Assay creator: Mojca Juteršek Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T21_SXPsysbio
Study: _S_P4_CoExpNetViz
