scripts/gffreadScript.txt Version 2
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP10-newG-DE/_A_07_NbAUSv1-0-InterPro/
SEEK ID: https://fairdomhub.org/data_files/5142?version=2
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gffreadScript.txt
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gffread -x /DATA/mojcaj/CDSfasta.fa -g /DATA/mojcaj/NbAUSv1.0_2019-11-29.fasta /DATA/mojcaj/NbAUSv1.0_AUGUSTUS-genes_2019-12-02.gff3 gffread -y /DATA/mojcaj/ProteinFasta.fa -g /DATA/mojcaj/NbAUSv1.0_2019-11-29.fasta /DATA/mojcaj/NbAUSv1.0_AUGUSTUS-genes_2019-12-02.gff3 Error: discarding overlapping duplicate gene feature (2717287-2733624) with ID=g65341 Error: discarding overlapping duplicate gene feature (89061700-89064143) with ID=g69190 Error: discarding overlapping duplicate gene feature (58785328-58791664) with ID=g67772 Error: discarding overlapping duplicate gene feature (74981446-74988480) with ID=g68435 Error: discarding overlapping duplicate gene feature (96744896-96751516) with ID=g69553 Error: discarding overlapping duplicate gene feature (144349719-144358669) with ID=g71652 Error: discarding overlapping duplicate gene feature (138441964-138445991) with ID=g71354 Error: discarding overlapping duplicate gene feature (170635340-170641786) with ID=g73066 Error: discarding overlapping duplicate gene feature (34376450-34381501) with ID=g81899 Error: discarding overlapping duplicate gene feature (57141738-57147615) with ID=g83005 Error: discarding overlapping duplicate gene feature (103066550-103074714) with ID=g85652 Error: discarding overlapping duplicate gene feature (67313257-67317081) with ID=g83453 Error: discarding overlapping duplicate gene feature (32633066-32647538) with ID=g95465 Error: discarding overlapping duplicate gene feature (53305577-53313953) with ID=g96331 Error: discarding overlapping duplicate gene feature (90885954-90893041) with ID=g98321 Error: discarding overlapping duplicate gene feature (44363981-44370318) with ID=g128300 Error: discarding overlapping duplicate gene feature (91906771-91915053) with ID=g130657 Error: discarding overlapping duplicate gene feature (92765285-92776476) with ID=g130707 Error: discarding overlapping duplicate gene feature (101861816-101866631) with ID=g131275 Error: discarding overlapping duplicate gene feature (32847246-32850995) with ID=g60295 Error: discarding overlapping duplicate gene feature (74056687-74062808) with ID=g62578 Error: discarding overlapping duplicate gene feature (3502625-3514276) with ID=g87650 Error: discarding overlapping duplicate gene feature (22182430-22192485) with ID=g88555 Error: discarding overlapping duplicate gene feature (64321707-64327410) with ID=g90611 Error: discarding overlapping duplicate gene feature (99722685-99731664) with ID=g92363 Error: discarding overlapping duplicate gene feature (38032590-38056596) with ID=g1977 Error: discarding overlapping duplicate gene feature (74838428-74845952) with ID=g4066 Error: discarding overlapping duplicate gene feature (10999567-11004415) with ID=g106854 Error: discarding overlapping duplicate gene feature (24948791-24955000) with ID=g107502 Error: discarding overlapping duplicate gene feature (112639936-112651097) with ID=g111973 Error: discarding overlapping duplicate gene feature (8479634-8489031) with ID=g101119 Error: discarding overlapping duplicate gene feature (12844006-12863720) with ID=g101427 Error: discarding overlapping duplicate gene feature (89389643-89403356) with ID=g104909 Error: discarding overlapping duplicate gene feature (104973636-104985361) with ID=g79630 Error: discarding overlapping duplicate gene feature (11924765-11932508) with ID=g7028 Error: discarding overlapping duplicate gene feature (66523916-66534745) with ID=g9510 Error: discarding overlapping duplicate gene feature (155708737-155714551) with ID=g13494 Error: discarding overlapping duplicate gene feature (157264077-157268724) with ID=g13571 Error: discarding overlapping duplicate gene feature (134669772-134679653) with ID=g12365 Error: discarding overlapping duplicate gene feature (142551874-142558204) with ID=g12768 Error: discarding overlapping duplicate gene feature (147966582-147979526) with ID=g13030 Error: discarding overlapping duplicate gene feature (165782374-165784991) with ID=g14025 Error: discarding overlapping duplicate gene feature (168683197-168690174) with ID=g14209 Error: discarding overlapping duplicate gene feature (86728088-86750278) with ID=g33283 Error: discarding overlapping duplicate gene feature (60681546-60694080) with ID=g32149 Error: discarding overlapping duplicate gene feature (132488737-132519734) with ID=g43463 Error: discarding overlapping duplicate gene feature (137890089-137900822) with ID=g43867 Error: discarding overlapping duplicate gene feature (75651119-75678242) with ID=g41009 Error: discarding overlapping duplicate gene feature (93881296-93889316) with ID=g41783 Error: discarding overlapping duplicate gene feature (41448726-41459345) with ID=g16960 Error: discarding overlapping duplicate gene feature (70547161-70559339) with ID=g18470 Error: discarding overlapping duplicate gene feature (119162620-119172116) with ID=g20646 Error: discarding overlapping duplicate gene feature (133750874-133786654) with ID=g21274 Error: discarding overlapping duplicate gene feature (24233709-24238932) with ID=g46850 Error: discarding overlapping duplicate gene feature (8234692-8243414) with ID=g46098 Error: discarding overlapping duplicate gene feature (65541629-65548785) with ID=g48597 Error: discarding overlapping duplicate gene feature (114474780-114481867) with ID=g50591 Error: discarding overlapping duplicate gene feature (58839505-58843474) with ID=g122753 Error: discarding overlapping duplicate gene feature (82106361-82116512) with ID=g123875 Error: discarding overlapping duplicate gene feature (81597382-81605920) with ID=g116599 Error: discarding overlapping duplicate gene feature (7760515-7764254) with ID=g22826 Error: discarding overlapping duplicate gene feature (10020706-10027925) with ID=g22965 Error: discarding overlapping duplicate gene feature (21934239-21941144) with ID=g23824 Error: discarding overlapping duplicate gene feature (28913686-28922959) with ID=g24338 Error: discarding overlapping duplicate gene feature (105614646-105621013) with ID=g27989 Error: discarding overlapping duplicate gene feature (52134478-52140114) with ID=g25768 Error: discarding overlapping duplicate gene feature (74209086-74219346) with ID=g26820
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Views: 1037 Downloads: 45
Created: 10th Apr 2022 at 07:51
Last updated: 21st Sep 2022 at 10:46
AttributionsNone
Version History
Version 2 (latest) Created 10th Apr 2022 at 08:49 by Marko Petek
uploaded again due to connection drop when uploading
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: P4_SxP10-newG-DE Title: SxPv1.0 RNA-seq analysis using the new Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the not yet published now high quality genome of Nicotiana benthamiana from the Newcotiana project. 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_toNewGenome-CLC-mapping, _A_02_limmavoomDE-R, _A_02a_limmavoomDEbylines-R, _A_03_NewGenome-MapMan, _A_04_GSEA-Stat, _A_05_Phenotype_analysis-Stat, _A_06_SxPv1-0_Illumina-Centrifuge, _A_07_NbAUSv1-0-InterPro, _S_P4_SxP10-newG-DE-files
Short Name: 07_NbAUSv1-0-InterPro Assay Class: DRY Assay Type: InterPro Title: InterProScan annotation of the new Nb genome - NbAUSv1.0 Description: * pISA Assay creation date: 2021-10-21 pISA Assay creator: * Phenodata: ../../phenodata_20191104.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T21_SXPsysbio
Study: _S_P4_SxP10-newG-DE
