_A_02_cdhit_3cvs-GFFmerged

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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:

DOI: 10.15490/fairdomhub.1.assay.1263.2

Zenodo URL: None

Created at: 11th Apr 2020 at 23:34

Contents

/input/path_to_files.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • path_to_files.txt

/input/Solanum_tuberosum_ITAG_DM_v1_descriptions_v2.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • Solanum_tuberosum_ITAG_DM_v1_descriptions_v2.txt

/input/Solanum_tuberosum_PGSC_DM_v4.04_converterWithDescriptions.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

/input/StPGSC4.04n_seq_4_PGSC-p-rep_ITAG-pep_gff-2019-04-23.fasta

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

/intermediate/singletons.DM.seqID.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • singletons.DM.seqID.txt

/intermediate/singletons.seqID.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • singletons.seqID.txt

/intermediate/singletons.tetra.seqID.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • singletons.tetra.seqID.txt

/intermediate/stCuSTr_cds_repAlt_cdhitEST-conda_aS.75_c.90.clstr

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

/intermediate/stPanTr_aa_singletons_DM_on_tetra_aS.45_c.90.clstr

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr_aa_singletons_DM_on_tetra_aS.45_c.90.clstr

/intermediate/stPanTr_aa_singletons_tetra_on_DM_aS.45_c.90.clstr

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr_aa_singletons_tetra_on_DM_aS.45_c.90.clstr

/output/5cv_weak-components.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • 5cv_weak-components.txt

/output/5cv_weak-components_withAnnotation.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • 5cv_weak-components_withAnnotation.tsv

/output/annot.alias.aa.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • annot.alias.aa.tsv

/output/annot.alias.cds.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • annot.alias.cds.tsv

/output/cdhit-est_rep-alt_aS.75_c.90_pairs.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • cdhit-est_rep-alt_aS.75_c.90_pairs.tsv

/output/cdhit-est_representativesMatched_aS.75_c.90.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • cdhit-est_representativesMatched_aS.75_c.90.tsv

/output/cdhit-est_singletons_aS.75_c.90.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • cdhit-est_singletons_aS.75_c.90.tsv

/output/stPanTr-clusters.tsv

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr-clusters.tsv

/output/trueSingle.DM.ID

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • trueSingle.DM.ID

/output/trueSingle.polyploid.ID

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • trueSingle.polyploid.ID

/output/VennDiagrams/stPanTr_geneCount_weak-components.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr_geneCount_weak-components.tiff

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr_geneCount_weak-components_rep.tiff

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep_perc.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr_geneCount_weak-components_rep_perc.tiff

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep+alt.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr_geneCount_weak-components_rep alt.tiff

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep+alt_and_stCuSTr_alt.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr_geneCount_weak-components_rep alt_and_stCuSTr_alt.tiff

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep+alt_and_stCuSTr_alt_perc.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr_geneCount_weak-components_rep alt_and_stCuSTr_alt_perc.tiff

/output/VennDiagrams/stPanTr_geneCount_weak-components_rep+alt_perc.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr_geneCount_weak-components_rep alt_perc.tiff

/output/VennDiagrams/stPanTr_geneCount_weak-components_repOnly.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr_geneCount_weak-components_repOnly.tiff

/output/VennDiagrams/stPanTr+stCuSTr_geneCount_weak-components.tiff

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • stPanTr stCuSTr_geneCount_weak-components.tiff

/scripts/01.1_commands-CDHIT-EST.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • 01.1_commands-CDHIT-EST.txt

/scripts/01.2_commands-CDHIT-2D.txt

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • 01.2_commands-CDHIT-2D.txt

/scripts/02_cd-hit-est_cdhit-2d.html

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • 02_cd-hit-est_cdhit-2d.html

/scripts/03_stPanTr_components_all.html

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • 03_stPanTr_components_all.html

/scripts/04_summary_stPanTr_v4.html

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • 04_summary_stPanTr_v4.html

/reports/SupplementaryFigure4.pdf

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/

  • SupplementaryFigure4.pdf

/reports/cvID_group-Rplot.pdf

No description specified

  • cvID_group-Rplot.pdf

/reports/cv_group-Rplot.pdf

No description specified

  • cv_group-Rplot.pdf

/reports/SupplementaryTableS7

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/

  • SupplementaryTableS7-Paralogue_cluster_information.xlsx

/_Assay_METADATA.TXT

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • _Assay_METADATA.TXT

/input/README.MD

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • README.MD

/output/README.MD

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • README.MD

/output/supplements/myPlot001.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot001.pdf

/output/supplements/myPlot002.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot002.pdf

/output/supplements/myPlot003.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot003.pdf

/output/supplements/myPlot004.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot004.pdf

/output/supplements/myPlot005.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot005.pdf

/output/supplements/myPlot006.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot006.pdf

/output/supplements/myPlot007.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot007.pdf

/output/supplements/myPlot008.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot008.pdf

/output/supplements/myPlot009.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot009.pdf

/output/supplements/myPlot010.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot010.pdf

/output/supplements/myPlot011.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot011.pdf

/output/supplements/myPlot012.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot012.pdf

/output/supplements/myPlot013.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot013.pdf

/output/supplements/myPlot014.pdf

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • myPlot014.pdf

/README.MD

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • README.MD

/scripts/02_cd-hit-est_cdhit-2d.Rmd

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • 02_cd-hit-est_cdhit-2d.Rmd

/scripts/03_stPanTr_components_all.Rmd

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • 03_stPanTr_components_all.Rmd

/scripts/04_summary_stPanTr_v4.Rmd

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • 04_summary_stPanTr_v4.Rmd

/scripts/README.MD

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

  • README.MD
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Citation
Blejec, A., & Zagorscak, M. (2020). _A_02_cdhit_3cvs-GFFmerged. FAIRDOMHub. https://doi.org/10.15490/FAIRDOMHUB.1.ASSAY.1263.2
Snapshots
Snapshot 2 (11th Apr 2020) DOI
Snapshot 1 (25th Mar 2020) DOI
Activity

Views: 948   Downloads: 13

Created: 11th Apr 2020 at 23:34

Last updated: 11th Apr 2020 at 23:39

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