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59 Assays visible to you, out of a total of 59

_A_02_components_1_3cvs-gffmerged

_p_stRT

paralogue clusters on pantranscriptome paralogue clusters on pantranscriptome

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/3cvs_sequences_keep.txt.gz, /input/pantr_aa.fasta.gz, /input/pantr_cds.fasta.gz, /input/pantr_tr.fasta.gz, /input/phureja_sequences_keep.txt.gz, /output/stPanTr_aa_alternatives.fasta.gz, /output/stPanTr_aa_representatives.fasta.gz, /output/stPanTr_cds_alternatives.fasta.gz, /output/stPanTr_cds_representatives.fasta.gz, /output/stPanTr_tr_alternatives.fasta.gz, /output/stPanTr_tr_representatives.fasta.gz, /scripts/i1.0_copy-to-input.txt, /scripts/i1.2_parse-fasta-files-pt1.pl, /scripts/i1.2_parse-fasta-files-pt2.pl, /scripts/i1.3_parse-headers.pl, /scripts/i2.1_prepare-network.pl, /scripts/i2.3_parse-weak-components.pl, /scripts/i2.4_prepare-rep-component-table.pl, /scripts/i3.1_prepare-fastas-pt1.pl, /scripts/i4.1_compress-fastas.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:18, Last updated: 10th Nov 2019 at 23:19

_A_01_evigene_1_3cvs-gffmerged

_p_stRT

tr2aacds on cv rep and gffmerged tr2aacds on cv rep and gffmerged

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_04_stPanTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/StPGSC4.04n_PGSC-ITAG-merged_representat..., /input/StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_gf..., /input/path_to_files.txt, /output/2019-08-05_3cv_gffmerged_cds_tr2ac1_log..., /output/3cv_gffmerged_cds.tr2aacds.log.gz, /output/3cv_gffmerged_cds.trclass.gz, /output/3cv_gffmerged_cds.trclass.sum.txt.gz, /output/dropset/3cv_gffmerged_cds.drop.aa.gz, /output/dropset/3cv_gffmerged_cds.drop.cds.gz, /output/dropset/3cv_gffmerged_cds.drop.fasta.gz, /output/inputset/3cv_gffmerged_cds.aa.gz, /output/inputset/3cv_gffmerged_cds.aa.qual.gz, /output/inputset/3cv_gffmerged_cds.cds.gz, /output/okayset/3cv_gffmerged_cds.okalt.aa.gz, /output/okayset/3cv_gffmerged_cds.okalt.cds.gz, /output/okayset/3cv_gffmerged_cds.okalt.fasta.gz, /output/okayset/3cv_gffmerged_cds.okay.aa.gz, /output/okayset/3cv_gffmerged_cds.okay.cds.gz, /output/okayset/3cv_gffmerged_cds.okay.fasta.gz, /output/retrieve/diff.aa.IDs.txt.gz, /output/retrieve/diff.cds.IDs.txt.gz, /output/retrieve/diff.tr.IDs.txt.gz, /scripts/01_run_3cv_gffmerged_cds_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:16, Last updated: 10th Nov 2019 at 23:18

_A__S_04_stPanTr-files

_p_stRT

Solanum tuberosum Pan-Transcriptome Solanum tuberosum Pan-Transcriptome

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_STRT-1

Study: _S_04_stPanTr

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:16, Last updated: 10th Nov 2019 at 23:16

_p_stRT

BUSCO post filtering and reassignment BUSCO post filtering and reassignment

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/BUSCOall_embryophyta_odb9.tsv, /output/short_summary.tar, /scripts/run_BUSCO_commands.sh, /transfer/evg_out.tsv

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:16, Last updated: 10th Nov 2019 at 23:16

_A_04_TransRate

_p_stRT

TransRate post filtering and reassignment TransRate post filtering and reassignment

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/Desiree_transrate_usingReference.log, /output/Desiree_transrate_usingReference_assemb..., /output/PW363_transrate_usingReference.log, /output/PW363_transrate_usingReference_assembli..., /output/Rywal_transrate_usingReference.log, /output/Rywal_transrate_usingReference_assembli..., /scripts/run_TransRate_commands.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:15, Last updated: 10th Nov 2019 at 23:16

_A_03.2_components

_p_stRT

Components: tr2aacds headers, cdhit-2d Components: tr2aacds headers, cdhit-2d; postfiltering redefinition of paralogue clusters

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /intermediate_4_cdhit-2d.tar.gz, /output/3cv_cdhit-2d_weak-components.txt.gz, /output/3cv_cdhit-2d_weak-components_alias.txt.gz, /output/fasta_1A_rep-per-cv/stCuSTr-D_aa_repres..., /output/fasta_1A_rep-per-cv/stCuSTr-D_cds_repre..., /output/fasta_1A_rep-per-cv/stCuSTr-D_tr_repres..., /output/fasta_1A_rep-per-cv/stCuSTr-P_aa_repres..., /output/fasta_1A_rep-per-cv/stCuSTr-P_cds_repre..., /output/fasta_1A_rep-per-cv/stCuSTr-P_tr_repres..., /output/fasta_1A_rep-per-cv/stCuSTr-R_aa_repres..., /output/fasta_1A_rep-per-cv/stCuSTr-R_cds_repre..., /output/fasta_1A_rep-per-cv/stCuSTr-R_tr_repres..., /output/fasta_1B_alt-per-cv/stCuSTr-D_aa_altern..., /output/fasta_1B_alt-per-cv/stCuSTr-D_cds_alter..., /output/fasta_1B_alt-per-cv/stCuSTr-D_tr_altern..., /output/fasta_1B_alt-per-cv/stCuSTr-P_aa_altern..., /output/fasta_1B_alt-per-cv/stCuSTr-P_cds_alter..., /output/fasta_1B_alt-per-cv/stCuSTr-P_tr_altern..., /output/fasta_1B_alt-per-cv/stCuSTr-R_aa_altern..., /output/fasta_1B_alt-per-cv/stCuSTr-R_cds_alter..., /output/fasta_1B_alt-per-cv/stCuSTr-R_tr_altern..., /output/fasta_2_all-per-cv/stCuSTr-D_aa_all.fas..., /output/fasta_2_all-per-cv/stCuSTr-D_cds_all.fa..., /output/fasta_2_all-per-cv/stCuSTr-D_tr_all.fas..., /output/fasta_2_all-per-cv/stCuSTr-P_aa_all.fas..., /output/fasta_2_all-per-cv/stCuSTr-P_cds_all.fa..., /output/fasta_2_all-per-cv/stCuSTr-P_tr_all.fas..., /output/fasta_2_all-per-cv/stCuSTr-R_aa_all.fas..., /output/fasta_2_all-per-cv/stCuSTr-R_cds_all.fa..., /output/fasta_2_all-per-cv/stCuSTr-R_tr_all.fas..., /output/fasta_3A_utrorfs-per-cv.tar.gz, /output/fasta_3B_eliminated-per-cv.tar.gz, /scripts/i1.0_copy-to-input.txt, /scripts/i1.1_parse-filtered-lists.pl, /scripts/i1.2_parse-fasta-files-pt1.pl, /scripts/i1.2_parse-fasta-files-pt2.pl, /scripts/i1.3_parse-headers.pl, /scripts/i2.1_prepare-network.pl, /scripts/i2.2_prepare-filter-master-file.pl, /scripts/i2.3_parse-n-filter-weak-components.pl, /scripts/i2.4_prepare-rep-component-table.pl, /scripts/i3.1_prepare-fastas-pt1.pl, /scripts/i3.2_prepare-fastas-pt2.pl, /scripts/i4.1_cdhit-2d.sh, /scripts/i5.1_parse-cdhit-2d.sh, /scripts/i5.2_parse-cdhit-2d-weak-components.Rmd, /scripts/i5.3_prepare-fastas.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:13, Last updated: 10th Nov 2019 at 23:15

_A_03.1_filtering

_p_stRT

Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate/intermediate-2-validate-removal.t..., /output/Desiree_tr.cds.tsv.gz, /output/PW363_tr.cds.tsv.gz, /output/Rywal_tr.cds.tsv.gz, /reports/03.1_Rywal_combo_withFiltering.html, /reports/03.2_PW363_combo_withFiltering.html, /reports/03.3_Desiree_combo_withFiltering.html, /scripts/01_ID_length_pairs.sh, /scripts/02_get_otherFiles.sh, /scripts/03.1_Rywal_combo_withFiltering.Rmd, /scripts/03.2_PW363_combo_withFiltering.Rmd, /scripts/03.3_Desiree_combo_withFiltering.Rmd, /scripts/04_summary.sh, /scripts/05_validate_removal.sh, /scripts/06_archive_files.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:12, Last updated: 10th Nov 2019 at 23:12

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