/_p_stRT_TREE.TXT Version 2
_p_stRT
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_p_stRT_TREE.TXT
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O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_stRT
Folder PATH listing for volume Skupni
Volume serial number is 8EBF-0990
O:.
| common.ini
| d.tmp
| FST.txt
| makeInvestigation.bat
| Metadata_files.md
| meta_I_Template.txt
| README.MD
| showMetadata.bat
| showTree.bat
| t.tmp
| TREE.TXT
| xcheckMetadata.bat
| xCheckMetadata.md
| _PROJECT_METADATA.TXT
| _p_stRT_TREE.TXT
|
+---presentations
| README.MD
|
+---reports
| README.MD
|
\---_I_STRT
| common.ini
| makeStudy.bat
| meta_S_Template.txt
| phenodata_20191022.txt
| README.MD
| showMetadata.bat
| showTree.bat
| xcheckMetadata.bat
| _INVESTIGATION_METADATA.TXT
|
+---presentations
| README.MD
|
+---reports
| README.MD
|
+---_S_01_sequences
| | common.ini
| | makeAssay.bat
| | meta_A_Template.txt
| | README.MD
| | showMetadata.bat
| | showTree.bat
| | xcheckMetadata.bat
| | _STUDY_METADATA.TXT
| |
| \---reports
| README.MD
| SupplementaryTableS1-Input_sequences_information.xlsx
|
+---_S_02_denovo
| | common.ini
| | makeAssay.bat
| | meta_A_Template.txt
| | README.MD
| | showMetadata.bat
| | showTree.bat
| | xcheckMetadata.bat
| | _STUDY_METADATA.TXT
| |
| \---reports
| README.MD
| SupplementaryTableS2-Primary_potato_transcriptome_assemblies.xlsx
|
+---_S_03_stCuSTr
| | common.ini
| | makeAssay.bat
| | meta_A_Template.txt
| | README.MD
| | showMetadata.bat
| | showTree.bat
| | xcheckMetadata.bat
| | _STUDY_METADATA.TXT
| |
| +---reports
| | README.MD
| |
| +---_A_01_evigene
| | | intermediate_tr2aacds_Desiree.tar.gz
| | | intermediate_tr2aacds_PW363.tar.gz.aa
| | | intermediate_tr2aacds_PW363.tar.gz.ab
| | | intermediate_tr2aacds_Rywal.tar.gz
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---output
| | | 3cvs_aa.fasta.gz
| | | 3cvs_cds.fasta.gz
| | | 3cvs_tr.fasta.gz
| | |
| | \---scripts
| | 01_run_commands.sh
| | my_tr2aacds.sh
| | README.MD
| | run_tr2aacds.sh
| |
| +---_A_02.1_BUSCO
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---output
| | | Desiree_assemblies.txt
| | | Desiree_repAlt.txt
| | | PW363_assemblies.txt
| | | PW363_repAlt.txt
| | | Rywal_assemblies.txt
| | | Rywal_rep.aa.txt
| | | Rywal_rep.tr.txt
| | | Rywal_repAlt.txt
| | |
| | \---scripts
| | 00_get_tools_and_export_paths.txt
| | 01_run_BUSCO.sh
| | README.MD
| |
| +---_A_02.2_assembly-contribution-count
| | | intermediate_Desiree.tar.gz
| | | intermediate_PW363.tar.gz
| | | intermediate_Rywal.tar.gz
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---output
| | | Desiree_cnt_assemblies.txt
| | | PW363_cnt_assemblies.txt
| | | Rywal_cnt_assemblies.txt
| | |
| | +---reports
| | | Figure3.pdf
| | | SupplementaryFigure1.pdf
| | | SupplementaryFigure2.pdf
| | |
| | \---scripts
| | countDesiree.sh
| | countPW363.sh
| | countRywal.sh
| |
| +---_A_02.3_InterProScan
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---intermediate
| | | +---Desiree_IPS
| | | | all.okalt.aa.tsv
| | | | all.okay.aa.tsv
| | | |
| | | +---PW363_IPS
| | | | all.okalt.aa.tsv
| | | | all.okay.aa.tsv
| | | |
| | | \---Rywal_IPS
| | | all.okalt.aa.tsv
| | | all.okay.aa.tsv
| | |
| | +---output
| | | Desiree_IPS_filtered_aggregated_filtered.tsv
| | | PW363_IPS_filtered_aggregated_filtered.tsv
| | | Rywal_IPS_filtered_aggregated_filtered.tsv
| | |
| | +---reports
| | | IPS_PowerQuery_PivotTable.xlsx
| | |
| | \---scripts
| | 01_potato_tr_evigene_IPS_commands.txt
| | 02_reshape_merge_aggregate_filter.Rmd
| |
| +---_A_02.4_STAR
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---output
| | | output_STAR_logs-n-SJ.tar.gz
| | |
| | \---scripts
| | STAR_commands.txt
| |
| +---_A_02.5_STARlong_matchAnnot
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---output
| | | output_1_STARlong-logs-n-SJ.tar.gz
| | | output_2_matchAnnot-parsed-txt.tar.gz
| | | README.MD
| | |
| | \---scripts
| | STARlongMatchAnnot_commands_ENCODE_denovo_param.txt
| |
| +---_A_02.6_TransRate
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---output
| | | Desiree_initial_transrate_usingReference.log
| | | Desiree_initial_transrate_usingReference_assemblies.csv
| | | PW363_initial_transrate_usingReference.log
| | | PW363_initial_transrate_usingReference_assemblies.csv
| | | Rywal_initial_transrate_usingReference.log
| | | Rywal_initial_transrate_usingReference_assemblies.csv
| | |
| | \---scripts
| | run_TransRate_commands.sh
| | Transrate_GitHub_README.md
| |
| +---_A_02.7_VecScreen
| | | intermediate.tar.gz
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---output
| | | Desiree_vecscreen.tsv
| | | PW363_vecscreen.tsv
| | | Rywal_vecscreen.tsv
| | |
| | \---scripts
| | 01_get_input.sh
| | 02_VecScreenPlus_blastn.sh
| | ENCH_sumablastplus.pl
| |
| +---_A_02.8_DIAMOND
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---output
| | | Desiree.cds_Solanaceae.out.ENCHformat_top1.tsv.gz
| | | Desiree.cds_solanumTuberosum.out.ENCHformat_top1.tsv.gz
| | | Desiree.cds_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
| | | Desiree.cds_SwissProt_TrEMBL.out.ENCHformat_top1.tsv.gz
| | | Desiree.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
| | | Desiree.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
| | | Desiree.tr_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
| | | Desiree.tr_SwissProt_TrEMBL.out.ENCHformat_top1.tsv.gz
| | | Desiree_rescued.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
| | | Desiree_rescued.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
| | | Desiree_rescued.tr_sprot_trembl.out.ENCHformat_top1.tsv.gz
| | | Desiree_rescued.tr_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
| | | PW363.cds_Solanaceae.out.ENCHformat_top1.tsv.gz
| | | PW363.cds_solanumTuberosum.out.ENCHformat_top1.tsv.gz
| | | PW363.cds_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
| | | PW363.cds_SwissProt_TrEMBL.out.ENCHformat_top1.tsv.gz
| | | PW363.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
| | | PW363.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
| | | PW363.tr_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
| | | PW363.tr_SwissProt_TrEMBL.out.ENCHformat_top1.tsv.gz
| | | PW363_rescued.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
| | | PW363_rescued.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
| | | PW363_rescued.tr_sprot_trembl.out.ENCHformat_top1.tsv.gz
| | | PW363_rescued.tr_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
| | | Rywal.cds_Solanaceae.out.ENCHformat_top1.tsv.gz
| | | Rywal.cds_solanumTuberosum.out.ENCHformat_top1.tsv.gz
| | | Rywal.cds_sprot_trembl.out.ENCHformat_top1.tsv.gz
| | | Rywal.cds_Swissprot_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
| | | Rywal.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
| | | Rywal.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
| | | Rywal.tr_sprot_trembl.out.ENCHformat_top1.tsv.gz
| | | Rywal.tr_Swissprot_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
| | | Rywal_rescued.tr_Solanaceae.out.ENCHformat_top1.tsv.gz
| | | Rywal_rescued.tr_solanumTuberosum.out.ENCHformat_top1.tsv.gz
| | | Rywal_rescued.tr_sprot_trembl.out.ENCHformat_top1.tsv.gz
| | | Rywal_rescued.tr_SP_TrEMBL_plants.out.ENCHformat_top1.tsv.gz
| | |
| | \---scripts
| | 01_get_input.sh
| | 02_DIAMOND_commands.sh
| | 03_archive_files.sh
| |
| +---_A_03.1_filtering
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---intermediate
| | | intermediate-2-validate-removal.tar.gz
| | |
| | +---output
| | | | Desiree_tr.cds.tsv.gz
| | | | PW363_tr.cds.tsv.gz
| | | | Rywal_tr.cds.tsv.gz
| | | |
| | | \---other
| | | output_full.tar.gz
| | | output_summary.tar.gz
| | |
| | +---reports
| | | 03.1_Rywal_combo_withFiltering.html
| | | 03.2_PW363_combo_withFiltering.html
| | | 03.3_Desiree_combo_withFiltering.html
| | |
| | \---scripts
| | 01_ID_length_pairs.sh
| | 02_get_otherFiles.sh
| | 03.1_Rywal_combo_withFiltering.Rmd
| | 03.2_PW363_combo_withFiltering.Rmd
| | 03.3_Desiree_combo_withFiltering.Rmd
| | 04_summary.sh
| | 05_validate_removal.sh
| | 06_archive_files.sh
| |
| +---_A_03.2_components
| | | intermediate_4_cdhit-2d.tar.gz
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | README.MD
| | |
| | +---output
| | | | 3cv_cdhit-2d_weak-components.txt.gz
| | | | 3cv_cdhit-2d_weak-components_alias.txt.gz
| | | | fasta_3A_utrorfs-per-cv.tar.gz
| | | | fasta_3B_eliminated-per-cv.tar.gz
| | | | README.MD
| | | |
| | | +---fasta_1A_rep-per-cv
| | | | stCuSTr-D_aa_representatives.fasta.gz
| | | | stCuSTr-D_cds_representatives.fasta.gz
| | | | stCuSTr-D_tr_representatives.fasta.gz
| | | | stCuSTr-P_aa_representatives.fasta.gz
| | | | stCuSTr-P_cds_representatives.fasta.gz
| | | | stCuSTr-P_tr_representatives.fasta.gz
| | | | stCuSTr-R_aa_representatives.fasta.gz
| | | | stCuSTr-R_cds_representatives.fasta.gz
| | | | stCuSTr-R_tr_representatives.fasta.gz
| | | |
| | | +---fasta_1B_alt-per-cv
| | | | stCuSTr-D_aa_alternatives.fasta.gz
| | | | stCuSTr-D_cds_alternatives.fasta.gz
| | | | stCuSTr-D_tr_alternatives.fasta.gz
| | | | stCuSTr-P_aa_alternatives.fasta.gz
| | | | stCuSTr-P_cds_alternatives.fasta.gz
| | | | stCuSTr-P_tr_alternatives.fasta.gz
| | | | stCuSTr-R_aa_alternatives.fasta.gz
| | | | stCuSTr-R_cds_alternatives.fasta.gz
| | | | stCuSTr-R_tr_alternatives.fasta.gz
| | | |
| | | \---fasta_2_all-per-cv
| | | stCuSTr-D_aa_all.fasta.gz
| | | stCuSTr-D_cds_all.fasta.gz
| | | stCuSTr-D_tr_all.fasta.gz
| | | stCuSTr-P_aa_all.fasta.gz
| | | stCuSTr-P_cds_all.fasta.gz
| | | stCuSTr-P_tr_all.fasta.gz
| | | stCuSTr-R_aa_all.fasta.gz
| | | stCuSTr-R_cds_all.fasta.gz
| | | stCuSTr-R_tr_all.fasta.gz
| | |
| | \---scripts
| | i1.0_copy-to-input.txt
| | i1.1_parse-filtered-lists.pl
| | i1.2_parse-fasta-files-pt1.pl
| | i1.2_parse-fasta-files-pt2.pl
| | i1.3_parse-headers.pl
| | i2.1_prepare-network.pl
| | i2.2_prepare-filter-master-file.pl
| | i2.3_parse-n-filter-weak-components.pl
| | i2.4_prepare-rep-component-table.pl
| | i3.1_prepare-fastas-pt1.pl
| | i3.2_prepare-fastas-pt2.pl
| | i4.1_cdhit-2d.sh
| | i5.1_parse-cdhit-2d.sh
| | i5.2_parse-cdhit-2d-weak-components.Rmd
| | i5.3_prepare-fastas.sh
| |
| +---_A_04_TransRate
| | | README.MD
| | | showMetadata.bat
| | | showTree.bat
| | | xcheckMetadata.bat
| | | _Assay_METADATA.TXT
| | |
| | +---input
| | | path_to_files.txt
| | |
| | +---output
| | | Desiree_transrate_usingReference.log
| | | Desiree_transrate_usingReference_assemblies.csv
| | | PW363_transrate_usingReference.log
| | | PW363_transrate_usingReference_assemblies.csv
| | | Rywal_transrate_usingReference.log
| | | Rywal_transrate_usingReference_assemblies.csv
| | |
| | \---scripts
| | run_TransRate_commands.sh
| |
| \---_A_05_BUSCO
| | README.MD
| | showMetadata.bat
| | showTree.bat
| | xcheckMetadata.bat
| | _Assay_METADATA.TXT
| |
| +---input
| | path_to_files.txt
| |
| +---output
| | BUSCOall_embryophyta_odb9.tsv
| | short_summary.tar
| |
| +---scripts
| | run_BUSCO_commands.sh
| |
| \---transfer
| evg_out.tsv
|
\---_S_04_stPanTr
| common.ini
| makeAssay.bat
| meta_A_Template.txt
| README.MD
| showMetadata.bat
| showTree.bat
| xcheckMetadata.bat
| _STUDY_METADATA.TXT
|
+---reports
| README.MD
|
+---_A_01_evigene_1_3cvs-gffmerged
| | README.MD
| | showMetadata.bat
| | showTree.bat
| | xcheckMetadata.bat
| | _Assay_METADATA.TXT
| |
| +---input
| | path_to_files.txt
| | StPGSC4.04n_PGSC-ITAG-merged_representative-transcript_genes_2019-04-23.gtf.gz
| | StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_gff-2019-04-23.fasta.gz
| |
| +---output
| | | 2019-08-05_3cv_gffmerged_cds_tr2ac1_log.txt.gz
| | | 3cv_gffmerged_cds.tr2aacds.log.gz
| | | 3cv_gffmerged_cds.trclass.gz
| | | 3cv_gffmerged_cds.trclass.sum.txt.gz
| | |
| | +---dropset
| | | 3cv_gffmerged_cds.drop.aa.gz
| | | 3cv_gffmerged_cds.drop.cds.gz
| | | 3cv_gffmerged_cds.drop.fasta.gz
| | |
| | +---inputset
| | | 3cv_gffmerged_cds.aa.gz
| | | 3cv_gffmerged_cds.aa.qual.gz
| | | 3cv_gffmerged_cds.cds.gz
| | |
| | +---okayset
| | | 3cv_gffmerged_cds.okalt.aa.gz
| | | 3cv_gffmerged_cds.okalt.cds.gz
| | | 3cv_gffmerged_cds.okalt.fasta.gz
| | | 3cv_gffmerged_cds.okay.aa.gz
| | | 3cv_gffmerged_cds.okay.cds.gz
| | | 3cv_gffmerged_cds.okay.fasta.gz
| | |
| | \---retrieve
| | diff.aa.IDs.txt.gz
| | diff.cds.IDs.txt.gz
| | diff.tr.IDs.txt.gz
| |
| \---scripts
| 01_run_3cv_gffmerged_cds_commands.sh
| my_tr2aacds.sh
| README.MD
| run_tr2aacds.sh
|
+---_A_02_components_1_3cvs-gffmerged
| | README.MD
| | showMetadata.bat
| | showTree.bat
| | xcheckMetadata.bat
| | _Assay_METADATA.TXT
| |
| +---input
| | 3cvs_sequences_keep.txt.gz
| | pantr_aa.fasta.gz
| | pantr_cds.fasta.gz
| | pantr_tr.fasta.gz
| | phureja_sequences_keep.txt.gz
| |
| +---output
| | stPanTr_aa_alternatives.fasta.gz
| | stPanTr_aa_representatives.fasta.gz
| | stPanTr_cds_alternatives.fasta.gz
| | stPanTr_cds_representatives.fasta.gz
| | stPanTr_tr_alternatives.fasta.gz
| | stPanTr_tr_representatives.fasta.gz
| |
| +---reports
| \---scripts
| i1.0_copy-to-input.txt
| i1.2_parse-fasta-files-pt1.pl
| i1.2_parse-fasta-files-pt2.pl
| i1.3_parse-headers.pl
| i2.1_prepare-network.pl
| i2.3_parse-weak-components.pl
| i2.4_prepare-rep-component-table.pl
| i3.1_prepare-fastas-pt1.pl
| i4.1_compress-fastas.sh
|
+---_A_03_BUSCO_1_3cvs-gffmerged
| | README.MD
| | showMetadata.bat
| | showTree.bat
| | xcheckMetadata.bat
| | _Assay_METADATA.TXT
| |
| +---input
| | path_to_files.txt
| |
| +---output
| | BUSCO_stPanTr_embryophyta_odb9.tsv
| | short_summary.tar
| |
| \---scripts
| run_BUSCO_commands.sh
|
+---_A_04-MSA
| | README.MD
| | showMetadata.bat
| | showTree.bat
| | xcheckMetadata.bat
| | _Assay_METADATA.TXT
| |
| +---input
| | D_P_R_g.tar.gz
| | README.MD
| | selected_4_wc.tar.gz
| |
| +---other
| +---output
| | | 5cv_weak-components.txt
| | | README.MD
| | |
| | +---out_aa_ClustalOmega_selected_4_wc_150_off_5_28
| | | stPanTr_007290.txt.aligned
| | | stPanTr_007290.txt.aligned.mview.html
| | | stPanTr_007290.txt.fasta
| | | stPanTr_007290.txt.ph
| | | stPanTr_007290.txt_.err.txt
| | | stPanTr_007290.txt_myLog.txt
| | | stPanTr_028778.txt.aligned
| | | stPanTr_028778.txt.aligned.mview.html
| | | stPanTr_028778.txt.fasta
| | | stPanTr_028778.txt.ph
| | | stPanTr_028778.txt_.err.txt
| | | stPanTr_028778.txt_myLog.txt
| | | stPanTr_038338.txt.aligned
| | | stPanTr_038338.txt.aligned.mview.html
| | | stPanTr_038338.txt.fasta
| | | stPanTr_038338.txt.ph
| | | stPanTr_038338.txt_.err.txt
| | | stPanTr_038338.txt_myLog.txt
| | | stPanTr_079878.txt.aligned
| | | stPanTr_079878.txt.aligned.mview.html
| | | stPanTr_079878.txt.fasta
| | | stPanTr_079878.txt.ph
| | | stPanTr_079878.txt_.err.txt
| | | stPanTr_079878.txt_myLog.txt
| | |
| | +---out_cds_ClustalOmega_selected_4_wc_150_off_5_28
| | | stPanTr_007290.txt.aligned
| | | stPanTr_007290.txt.aligned.mview.html
| | | stPanTr_007290.txt.fasta
| | | stPanTr_007290.txt.ph
| | | stPanTr_007290.txt_.err.txt
| | | stPanTr_007290.txt_myLog.txt
| | | stPanTr_028778.txt.aligned
| | | stPanTr_028778.txt.aligned.mview.html
| | | stPanTr_028778.txt.fasta
| | | stPanTr_028778.txt.ph
| | | stPanTr_028778.txt_.err.txt
| | | stPanTr_028778.txt_myLog.txt
| | | stPanTr_038338.txt.aligned
| | | stPanTr_038338.txt.aligned.mview.html
| | | stPanTr_038338.txt.fasta
| | | stPanTr_038338.txt.ph
| | | stPanTr_038338.txt_.err.txt
| | | stPanTr_038338.txt_myLog.txt
| | | stPanTr_079878.txt.aligned
| | | stPanTr_079878.txt.aligned.mview.html
| | | stPanTr_079878.txt.fasta
| | | stPanTr_079878.txt.ph
| | | stPanTr_079878.txt_.err.txt
| | | stPanTr_079878.txt_myLog.txt
| | |
| | \---out_MAFFT_D_P_R_g_full_off_20_28
| | Merged.aa.html
| |
| +---reports
| | Figure4.pdf
| | README.MD
| | stPanTr_geneCount_paralogue-clusters.tiff
| | SupplementaryFigure3.pdf
| |
| +---scripts
| | 01_merge_all_wc.Rmd
| | 02_run_5cv.fasta_MSA.sh
| | MSA.py
| | print.sh
| |
| \---testSet
| | my.fasta
| |
| \---folderWithIds
| IDs1
| IDs2
|
\---_A_05_BUSCO-Stat
| README.MD
| showMetadata.bat
| showTree.bat
| xcheckMetadata.bat
| _Assay_METADATA.TXT
|
+---input
| path_to_files.txt
| README.MD
|
+---intermediate
| BUSCOall_embryophyta_odb9.tsv
| BUSCO_stPanTr_embryophyta_odb9.tsv
| evg_out.tsv
|
+---other
| README.MD
|
+---output
| README.MD
|
+---reports
| BUSCO1.pdf
| BUSCO_plots.html
| README.MD
|
\---scripts
BUSCO_plots.Rmd
README.MD
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Created: 6th Nov 2019 at 13:51
Last updated: 25th Nov 2019 at 23:27
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Version 2 (latest) Created 6th Nov 2019 at 16:01 by Maja Zagorscak
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https://orcid.org/0000-0001-7484-6031
https://orcid.org/0000-0002-1669-6482
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, INDIE - Biotechnological production of sustainable indole, _p_stRT, Public project, Playground, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture
Institutions: National Institute of Biology, NewHorizon
https://orcid.org/0000-0001-7484-6031
Projects: pISA-tree, HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, tst, tst2
Institutions: National Institute of Biology, tst
https://orcid.org/0000-0002-1669-6482
Computational Biologist and Biostatistician at Department of Biotechnology and Systems Biology, National Institute of Biology (NIB)
Advanced Programmes list for this Document with search and filtering
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
Advanced Projects list for this Document with search and filtering
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
