Assays

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24 Assays visible to you, out of a total of 24

_p_stRT

BUSCO on assemblies and tr2aacds output BUSCO on assemblies and 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, /input/path_to_files.txt, /output/Desiree_assemblies.txt, /output/Desiree_assemblies.txt, /output/Desiree_repAlt.txt, /output/Desiree_repAlt.txt, /output/PW363_assemblies.txt, /output/PW363_assemblies.txt, /output/PW363_repAlt.txt, /output/PW363_repAlt.txt, /output/Rywal_assemblies.txt, /output/Rywal_rep.aa.txt, /output/Rywal_rep.aa.txt, /output/Rywal_rep.tr.txt, /output/Rywal_rep.tr.txt, /output/Rywal_repAlt.txt, /output/Rywal_repAlt.txt, /scripts/00_get_tools_and_export_paths.txt, /scripts/00_get_tools_and_export_paths.txt, /scripts/01_run_BUSCO.sh, /scripts/01_run_BUSCO.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:06, Last updated: 19th Aug 2021 at 07:43

_p_stRT

EvidentialGene tr2aacds.pl VERSION 2016.07.11 See http://eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html

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, /input/path_to_files.txt, /input/path_to_files.txt, /input/path_to_files.txt, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_Rywal.tar.gz, /intermediate_tr2aacds_Rywal.tar.gz, /intermediate_tr2aacds_Rywal.tar.gz, /intermediate_tr2aacds_Rywal.tar.gz, /output/3cvs_aa.fasta.gz, /output/3cvs_aa.fasta.gz, /output/3cvs_aa.fasta.gz, /output/3cvs_aa.fasta.gz, /output/3cvs_cds.fasta.gz, /output/3cvs_cds.fasta.gz, /output/3cvs_cds.fasta.gz, /output/3cvs_tr.fasta.gz, /output/3cvs_tr.fasta.gz, /output/3cvs_tr.fasta.gz, /scripts/01_run_commands.sh, /scripts/01_run_commands.sh, /scripts/01_run_commands.sh, /scripts/my_tr2aacds.sh, /scripts/my_tr2aacds.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh, /scripts/run_tr2aacds.sh, /scripts/run_tr2aacds.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 22:39, Last updated: 13th Nov 2019 at 22:34

_A_02.6_TransRate

_p_stRT

TransRate stat on raw tr2aacds transcriptomes TransRate stat on raw tr2aacds transcriptomes, basic and reference-based

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, /input/path_to_files.txt, /output/Desiree_initial_transrate_usingReferenc..., /output/Desiree_initial_transrate_usingReferenc..., /output/Desiree_initial_transrate_usingReferenc..., /output/Desiree_initial_transrate_usingReferenc..., /output/PW363_initial_transrate_usingReference.log, /output/PW363_initial_transrate_usingReference.log, /output/PW363_initial_transrate_usingReference_..., /output/PW363_initial_transrate_usingReference_..., /output/Rywal_initial_transrate_usingReference.log, /output/Rywal_initial_transrate_usingReference_..., /scripts/run_TransRate_commands.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:08, Last updated: 13th Nov 2019 at 22:30

_A_02.5_STARlong_matchAnnot

_p_stRT

potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations

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, /input/path_to_files.txt, /output/output_1_STARlong-logs-n-SJ.tar.gz, /output/output_1_STARlong-logs-n-SJ.tar.gz, /output/output_2_matchAnnot-parsed-txt.tar.gz, /output/output_2_matchAnnot-parsed-txt.tar.gz, /scripts/STARlongMatchAnnot_commands_ENCODE_den..., /scripts/STARlongMatchAnnot_commands_ENCODE_den...

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:08, Last updated: 13th Nov 2019 at 22:30

_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: /_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.4_STAR/sho..., /input/path_to_files.txt, /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/output_STAR_logs-n-SJ.tar.gz, /scripts/STAR_commands.txt, /scripts/STAR_commands.txt

Snapshots: No snapshots

Created: 7th Nov 2019 at 10:03, Last updated: 13th Nov 2019 at 22:29

_A_02.3_InterProScan

_p_stRT

InterProScan on tr2aacds output InterProScan on 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, /input/path_to_files.txt, /intermediate/Desiree_IPS/all.okalt.aa.tsv, /intermediate/Desiree_IPS/all.okalt.aa.tsv, /intermediate/Desiree_IPS/all.okay.aa.tsv, /intermediate/Desiree_IPS/all.okay.aa.tsv, /intermediate/PW363_IPS/all.okalt.aa.tsv, /intermediate/PW363_IPS/all.okalt.aa.tsv, /intermediate/PW363_IPS/all.okay.aa.tsv, /intermediate/PW363_IPS/all.okay.aa.tsv, /intermediate/Rywal_IPS/all.okalt.aa.tsv, /intermediate/Rywal_IPS/all.okalt.aa.tsv, /intermediate/Rywal_IPS/all.okay.aa.tsv, /intermediate/Rywal_IPS/all.okay.aa.tsv, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd, /scripts/02_reshape_merge_aggregate_filter.Rmd

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:07, Last updated: 13th Nov 2019 at 22:29

_A_02.2_assembly-contribution-count

_p_stRT

assembly contribution count assembly contribution count, input/output tr2aacds

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, /input/path_to_files.txt, /intermediate_Desiree.tar.gz, /intermediate_Desiree.tar.gz, /intermediate_PW363.tar.gz, /intermediate_PW363.tar.gz, /intermediate_Rywal.tar.gz, /intermediate_Rywal.tar.gz, /output/Desiree_cnt_assemblies.txt, /output/Desiree_cnt_assemblies.txt, /output/PW363_cnt_assemblies.txt, /output/PW363_cnt_assemblies.txt, /output/Rywal_cnt_assemblies.txt, /output/Rywal_cnt_assemblies.txt, /scripts/countDesiree.sh, /scripts/countDesiree.sh, /scripts/countPW363.sh, /scripts/countPW363.sh, /scripts/countRywal.sh, /scripts/countRywal.sh

Snapshots: No snapshots

Created: 10th Nov 2019 at 23:06, Last updated: 13th Nov 2019 at 22:28

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