Assays

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829 Assays visible to you, out of a total of 1136

_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

_A_02.8_DIAMOND

_p_stRT

No description specified

Submitter: Andrej Blejec

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_STRT-1

Study: _S_03_stCuSTr

Organisms: No organisms

SOPs: No SOPs

Data files: /NA.TXT, /_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.8_DIAMOND/..., /input/path_to_files.txt, /output/Desiree.cds_SP_TrEMBL_plants.out.ENCHfo..., /output/Desiree.cds_Solanaceae.out.ENCHformat_t..., /output/Desiree.cds_SwissProt_TrEMBL.out.ENCHfo..., /output/Desiree.cds_SwissProt_TrEMBL.out.ENCHfo..., /output/Desiree.cds_solanumTuberosum.out.ENCHfo..., /output/Desiree.tr_SP_TrEMBL_plants.out.ENCHfor..., /output/Desiree.tr_Solanaceae.out.ENCHformat_to..., /output/Desiree.tr_SwissProt_TrEMBL.out.ENCHfor..., /output/Desiree.tr_solanumTuberosum.out.ENCHfor..., /output/Desiree_rescued.tr_SP_TrEMBL_plants.out..., /output/Desiree_rescued.tr_Solanaceae.out.ENCHf..., /output/Desiree_rescued.tr_solanumTuberosum.out..., /output/Desiree_rescued.tr_sprot_trembl.out.ENC..., /output/PW363.cds_SP_TrEMBL_plants.out.ENCHform..., /output/PW363.cds_Solanaceae.out.ENCHformat_top..., /output/PW363.cds_SwissProt_TrEMBL.out.ENCHform..., /output/PW363.cds_solanumTuberosum.out.ENCHform..., /output/PW363.tr_SP_TrEMBL_plants.out.ENCHforma..., /output/PW363.tr_Solanaceae.out.ENCHformat_top1..., /output/PW363.tr_SwissProt_TrEMBL.out.ENCHforma..., /output/PW363.tr_solanumTuberosum.out.ENCHforma..., /output/PW363_rescued.tr_SP_TrEMBL_plants.out.E..., /output/PW363_rescued.tr_Solanaceae.out.ENCHfor..., /output/PW363_rescued.tr_solanumTuberosum.out.E..., /output/PW363_rescued.tr_sprot_trembl.out.ENCHf..., /output/Rywal.cds_Solanaceae.out.ENCHformat_top..., /output/Rywal.cds_Swissprot_TrEMBL_plants.out.E..., /output/Rywal.cds_solanumTuberosum.out.ENCHform..., /output/Rywal.cds_sprot_trembl.out.ENCHformat_t..., /output/Rywal.tr_Solanaceae.out.ENCHformat_top1..., /output/Rywal.tr_Swissprot_TrEMBL_plants.out.EN..., /output/Rywal.tr_solanumTuberosum.out.ENCHforma..., /output/Rywal.tr_sprot_trembl.out.ENCHformat_to..., /output/Rywal_rescued.tr_SP_TrEMBL_plants.out.E..., /output/Rywal_rescued.tr_Solanaceae.out.ENCHfor..., /output/Rywal_rescued.tr_solanumTuberosum.out.E..., /output/Rywal_rescued.tr_sprot_trembl.out.ENCHf..., /scripts/01_get_input.sh, /scripts/02_DIAMOND_commands.sh, /scripts/03_archive_files.sh

Snapshots: No snapshots

Created: 7th Nov 2019 at 09:18, Last updated: 10th Nov 2019 at 23:12

_A_02.7_VecScreen

_p_stRT

VecScreen on raw tr2aacds output VecScreen and blastn on raw tr2aacds output

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.tar.gz, /output/Desiree_vecscreen.tsv, /output/PW363_vecscreen.tsv, /output/Rywal_vecscreen.tsv, /scripts/01_get_input.sh, /scripts/02_VecScreenPlus_blastn.sh, /scripts/ENCH_sumablastplus.pl

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:09, Last updated: 10th Nov 2019 at 23:09

(v.1.16.0-pre)

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