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545 items tagged with 'demo'.
  • Data files (544)
  • Presentations (1)
/input/README.MD
Test project 2021-08-20 22:56:43

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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: Test investigation 2021-08-20 23:06:07

Studies: Test study 2021-08-20 23:16:27

Assays: Test Assay 2021-08-20 23:19:14

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Created: 20th Aug 2021 at 21:25, Last updated: 20th Aug 2021 at 21:25
Views: 464, Downloads: 15
/output/annot_stCuSTr-P_cds_all.zip
_p_stRT

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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_09_annotation-GFFmerged

Download
Created: 13th May 2021 at 17:31, Last updated: 13th May 2021 at 17:32
Views: 641, Downloads: 21
/output/Desiree_SRR10416848/Log.final.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

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Created: 13th May 2021 at 17:31, Last updated: 13th May 2021 at 17:31
Views: 542, Downloads: 20
/intermediate/Desiree/genomeParameters.txt
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Andrej Blejec
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Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

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Created: 13th May 2021 at 17:31, Last updated: 13th May 2021 at 17:31
Views: 665, Downloads: 14
/output/PGSC_SRR10416848/Log.final.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

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Created: 13th May 2021 at 17:31, Last updated: 13th May 2021 at 17:31
Views: 658, Downloads: 17
/intermediate/trueSingle.DM.cds.fasta
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Andrej Blejec
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Creator: Andrej Blejec

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Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_08_centrifuge_3cvs-GFFmerged

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Created: 13th May 2021 at 17:31, Last updated: 13th May 2021 at 17:31
Views: 684, Downloads: 15
/scripts/annotate.sh
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Andrej Blejec
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Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_09_annotation-GFFmerged

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Created: 13th May 2021 at 17:31, Last updated: 13th May 2021 at 17:31
Views: 619, Downloads: 18
/output/Desiree_SRR10416849/Log.progress.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

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Created: 13th May 2021 at 17:31, Last updated: 13th May 2021 at 17:31
Views: 651, Downloads: 19
/intermediate/trueSingle.polyploid.tr.fasta
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Andrej Blejec
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Creator: Andrej Blejec

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Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_08_centrifuge_3cvs-GFFmerged

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Created: 13th May 2021 at 17:31, Last updated: 13th May 2021 at 17:31
Views: 646, Downloads: 13
/output/annot_stCuSTr-D_cds_all.zip
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_09_annotation-GFFmerged

Download
Created: 13th May 2021 at 17:31, Last updated: 13th May 2021 at 17:31
Views: 484, Downloads: 15
/intermediate/PGSC/chrNameLength.txt
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 17:29, Last updated: 13th May 2021 at 17:29
Views: 513, Downloads: 19
/intermediate/trueSingle.polyploid.cds.fasta
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_08_centrifuge_3cvs-GFFmerged

Download
Created: 13th May 2021 at 17:29, Last updated: 13th May 2021 at 17:29
Views: 515, Downloads: 17
/output/annot_stPanTr.aa.zip
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_09_annotation-GFFmerged

Download
Created: 13th May 2021 at 17:29, Last updated: 13th May 2021 at 17:29
Views: 657, Downloads: 17
/output/Desiree_SRR10416849/Log.progress.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 17:29, Last updated: 13th May 2021 at 17:29
Views: 435, Downloads: 14
/intermediate/PGSC/chrName.txt
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

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Created: 13th May 2021 at 17:29, Last updated: 13th May 2021 at 17:29
Views: 636, Downloads: 14
/intermediate/indexGFFmerged.log
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

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Created: 13th May 2021 at 17:29, Last updated: 13th May 2021 at 17:29
Views: 669, Downloads: 15
/output/annot_stCuSTr-D_aa_alternatives.zip
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_09_annotation-GFFmerged

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Created: 13th May 2021 at 17:29, Last updated: 13th May 2021 at 17:29
Views: 624, Downloads: 17
/output/trueSingle.polyploid.tr_kreport.txt
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_08_centrifuge_3cvs-GFFmerged

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Created: 13th May 2021 at 17:29, Last updated: 13th May 2021 at 17:29
Views: 526, Downloads: 12
/output/Desiree_SRR10416847/Log.final.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 17:28, Last updated: 13th May 2021 at 17:28
Views: 669, Downloads: 17
/output/annot_stCuSTr-P_tr_all.zip
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_09_annotation-GFFmerged

Download
Created: 13th May 2021 at 17:28, Last updated: 13th May 2021 at 17:28
Views: 615, Downloads: 16
/intermediate/gff-merged/chrName.txt
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 17:28, Last updated: 13th May 2021 at 17:28
Views: 636, Downloads: 15
/output/annot_stPanTr_alt.aa.zip
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_09_annotation-GFFmerged

Download
Created: 13th May 2021 at 17:28, Last updated: 13th May 2021 at 17:28
Views: 633, Downloads: 17
/output/annot_stCuSTr-D_tr_all.zip
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_09_annotation-GFFmerged

Download
Created: 13th May 2021 at 17:28, Last updated: 13th May 2021 at 17:28
Views: 583, Downloads: 15
/output/PW363_report.txt
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_08_centrifuge_3cvs-GFFmerged

Download
Created: 13th May 2021 at 17:28, Last updated: 13th May 2021 at 17:28
Views: 579, Downloads: 14
/output/gff-merged_SRR10416847/Log.progress.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 17:28, Last updated: 13th May 2021 at 17:28
Views: 635, Downloads: 17
/output/stCuSTr-P_tr_representatives_transrate_usingReference/stCuSTr-P_tr_representatives/StPGSC4.04n_seq_2_PGSC-t-rep_ITAG-cds_gff-2019-04-23.nin
_p_stRT

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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_06_tr_rep-transrate

Download
Created: 13th May 2021 at 17:28
Views: 510, Downloads: 16
/output/gff-merged_SRR10416849/Log.final.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 17:28, Last updated: 13th May 2021 at 17:28
Views: 558, Downloads: 16
/output/PGSC_drought123/Log.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 17:27, Last updated: 13th May 2021 at 17:28
Views: 509, Downloads: 18
/output/stCuSTr-R_tr_representatives_transrate_usingReference/stCuSTr-R_tr_representatives/stCuSTr-R_tr_representatives.nsq
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_06_tr_rep-transrate

Download
Created: 13th May 2021 at 11:57
Views: 543, Downloads: 16
/output/gff-merged_SRR10416847/Log.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 11:57, Last updated: 13th May 2021 at 11:57
Views: 535, Downloads: 16
/output/Desiree_drought123/Log.out
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Andrej Blejec
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Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 11:56, Last updated: 13th May 2021 at 11:56
Views: 565, Downloads: 20
/output/stCuSTr-P_tr_representatives_transrate_usingReference/stCuSTr-P_tr_representatives/StPGSC4.04n_seq_2_PGSC-t-rep_ITAG-cds_gff-2019-04-23.nhr
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_06_tr_rep-transrate

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Created: 13th May 2021 at 11:56
Views: 391, Downloads: 16
/output/annot_stCuSTr-P_aa_all.zip
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Andrej Blejec
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Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_09_annotation-GFFmerged

Download
Created: 13th May 2021 at 11:56, Last updated: 13th May 2021 at 11:56
Views: 541, Downloads: 19
/output/PGSC_SRR10416849/Log.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 11:56, Last updated: 13th May 2021 at 11:56
Views: 497, Downloads: 16
/output/PGSC_drought123/Log.progress.out
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Andrej Blejec
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Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_07_Desiree-mapping

Download
Created: 13th May 2021 at 11:56, Last updated: 13th May 2021 at 11:56
Views: 599, Downloads: 14
/output/stCuSTr-R_tr_representatives_transrate_usingReference/stCuSTr-R_tr_representatives/stCuSTr-R_tr_representatives.nin
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Andrej Blejec
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Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_06_tr_rep-transrate

Download
Created: 13th May 2021 at 11:56
Views: 675, Downloads: 12
/output/PGSC_DM_v3.4_transcript-update_representative_transrate_usingReference/PGSC_DM_v3.4_transcript-update_representative
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Andrej Blejec
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Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_06_tr_rep-transrate

Download
Created: 13th May 2021 at 11:46
Views: 532, Downloads: 12
/output/PGSC_DM_v3.4_transcript-update_representative_transrate_usingReference/PGSC_DM_v3.4_transcript-update_representative
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Andrej Blejec
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Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_06_tr_rep-transrate

Download
Created: 13th May 2021 at 11:43
Views: 513, Downloads: 19
/bla.r - study 148
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Andrej Blejec

Data file assoc with assay

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 20th Nov 2019 at 16:29
Views: 695, Downloads: 22
/bla.r
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Andrej Blejec

Data file assoc with assay

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_03_stCuSTr

Assays: _A_01_evigene

Download
Created: 20th Nov 2019 at 16:28
Views: 720, Downloads: 24
/bla.r
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Andrej Blejec

Testing of upload

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_03_stCuSTr

Assays: _A_01_evigene

Download
Created: 20th Nov 2019 at 16:22
Views: 762, Downloads: 30
/output/out_aa_ClustalOmega_selected_4_wc_150_off_5_28/stPanTr_007290.txt.ph
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Andrej Blejec

_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_04-MSA

Download
Created: 15th Nov 2019 at 00:26, Last updated: 15th Nov 2019 at 00:26
Views: 693, Downloads: 24
/output/Rywal_rep.tr.txt
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Andrej Blejec

Change license MIT-ni id

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_03_stCuSTr

Assays: _A_02.1_BUSCO

Download
Created: 15th Nov 2019 at 00:26, Last updated: 25th Nov 2019 at 15:26
Views: 716, Downloads: 26
/output/out_aa_ClustalOmega_selected_4_wc_150_off_5_28/stPanTr_028778.txt_myLog.txt
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Andrej Blejec

_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_04-MSA

Download
Created: 15th Nov 2019 at 00:26, Last updated: 15th Nov 2019 at 00:26
Views: 690, Downloads: 27
/output/out_aa_ClustalOmega_selected_4_wc_150_off_5_28/stPanTr_038338.txt_myLog.txt
_p_stRT

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Andrej Blejec

_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_04-MSA

Download
Created: 15th Nov 2019 at 00:25, Last updated: 15th Nov 2019 at 00:25
Views: 773, Downloads: 25
/output/PW363_tr.cds.tsv.gz
_p_stRT

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Andrej Blejec

_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_03_stCuSTr

Assays: _A_03.1_filtering

Download
Created: 15th Nov 2019 at 00:25
Views: 751, Downloads: 20
/scripts/06_archive_files.sh
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Andrej Blejec

_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.1_filtering

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_03_stCuSTr

Assays: _A_03.1_filtering

Download
Created: 15th Nov 2019 at 00:25, Last updated: 15th Nov 2019 at 00:25
Views: 695, Downloads: 18
/output/out_aa_ClustalOmega_selected_4_wc_150_off_5_28/stPanTr_007290.txt.fasta
_p_stRT

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Andrej Blejec

_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_04-MSA

Download
Created: 15th Nov 2019 at 00:25, Last updated: 15th Nov 2019 at 00:25
Views: 713, Downloads: 20
/output/out_aa_ClustalOmega_selected_4_wc_150_off_5_28/stPanTr_079878.txt.aligned.mview.html
_p_stRT

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Andrej Blejec

_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_04-MSA

Download
Created: 15th Nov 2019 at 00:25, Last updated: 15th Nov 2019 at 00:25
Views: 681, Downloads: 23
/output/5cv_weak-components.txt
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Andrej Blejec

_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_04_stPanTr

Assays: _A_04-MSA

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Created: 15th Nov 2019 at 00:25
Views: 700, Downloads: 24
/scripts/i1.2_parse-fasta-files-pt2.pl
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Andrej Blejec

_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.2_components

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_03_stCuSTr

Assays: _A_03.2_components

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Created: 15th Nov 2019 at 00:25, Last updated: 15th Nov 2019 at 00:25
Views: 701, Downloads: 19
/output/Desiree.cds_solanumTuberosum.out.ENCHformat_top1.tsv.gz
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Andrej Blejec

_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.8_DIAMOND

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_03_stCuSTr

Assays: _A_02.8_DIAMOND

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Created: 15th Nov 2019 at 00:24
Views: 700, Downloads: 19
/scripts/01_potato_tr_evigene_IPS_commands.txt
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Andrej Blejec

_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.3_InterProScan

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_03_stCuSTr

Assays: _A_02.3_InterProScan

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Created: 15th Nov 2019 at 00:24, Last updated: 15th Nov 2019 at 00:24
Views: 628, Downloads: 21
/scripts/i5.3_prepare-fastas.sh
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Andrej Blejec

_p_stRT/_I_STRT/_S_03_stCuSTr/_A_03.2_components

Creator: Andrej Blejec

Submitter: Andrej Blejec

Investigations: _I_STRT

Studies: _S_03_stCuSTr

Assays: _A_03.2_components

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Created: 15th Nov 2019 at 00:24, Last updated: 15th Nov 2019 at 00:24
Views: 630, Downloads: 13
/scripts/03_archive_files.sh
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/scripts/run_tr2aacds.sh
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/intermediate_tr2aacds_Desiree.tar.gz
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/scripts/run_tr2aacds.sh
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/intermediate_tr2aacds_Rywal.tar.gz
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/intermediate_tr2aacds_PW363.tar.gz.ab
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/intermediate_tr2aacds_Desiree.tar.gz
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/input/path_to_files.txt
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/reports/SupplementaryTableS1-Input_sequences_information.xlsx
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/intermediate_tr2aacds_Rywal.tar.gz
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/intermediate_tr2aacds_Desiree.tar.gz
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/output/PW363_initial_transrate_usingReference_assemblies.csv
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/output/Desiree_initial_transrate_usingReference_assemblies.csv
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/scripts/STARlongMatchAnnot_commands_ENCODE_denovo_param.txt
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/scripts/STAR_commands.txt
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/scripts/run_tr2aacds.sh
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/scripts/01_run_3cv_gffmerged_cds_commands.sh
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/output/retrieve/diff.tr.IDs.txt.gz
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/output/okayset/3cv_gffmerged_cds.okay.fasta.gz
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