The FAIRDOMHub

11 items tagged with 'Transcriptome'.

_A_03.2_components

_p_stRT

Assay: A03.2_components

Short Name: 03.2_components

Assay Class: DRY

Assay Type: components

Title: Components: tr2aacds headers, cdhit-2d

Description: Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters

pISA Assay creation date: 2019-10-22

pISA Assay creator: Ziva Ramsak

Phenodata: None

Featuredata:

Data:

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1171.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_4_cdhit-2d.tar.gz, /output/output.tar, /scripts/scripts.tar

Created: 7th Nov 2019 at 18:06, Last updated: 15th Nov 2019 at 21:07

_A_03.1_filtering

_p_stRT

Assay: A03.1_filtering

Short Name: 03.1_filtering

Assay Class: DRY

Assay Type: filtering

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

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

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1170.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate/intermediate.tar, /output/Desiree_tr.cds.tsv.gz, /output/PW363_tr.cds.tsv.gz, /output/Rywal_tr.cds.tsv.gz, /output/other/output_full.tar.gz, /output/other/output_summary.tar.gz, /reports/03.1_Rywal_combo_withFiltering.html, /reports/03.2_PW363_combo_withFiltering.html, /reports/03.3_Desiree_combo_withFiltering.html, /reports/SupplementaryTableS3, /reports/SupplementaryTableS4, /reports/SupplementaryTableS5, /scripts/scripts.tar

Created: 7th Nov 2019 at 18:04, Last updated: 18th Mar 2020 at 19:37

_A_02.8_DIAMOND

_p_stRT

Assay: A02.8_DIAMOND

Short Name: 02.8_DIAMOND

Assay Class: DRY

Assay Type: DIAMOND

Title: DIAMOND on raw tr2aacds output

Description: DIAMOND on raw tr2aacds output, both .cds and .tr; including lost and found

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1169.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Created: 7th Nov 2019 at 18:02, Last updated: 16th Nov 2019 at 12:28

_A_02.7_VecScreen

_p_stRT

Assay: A02.7_VecScreen

Short Name: 02.7_VecScreen

Assay Class: DRY

Assay Type: VecScreen

Title: VecScreen on raw tr2aacds output

Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1168.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum, Potato virus Y

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

Created: 7th Nov 2019 at 17:58, Last updated: 16th Nov 2019 at 12:37

_A_02.6_TransRate

_p_stRT

Assay: A02.6_TransRate

Short Name: 02.6_TransRate

Assay Class: DRY

Assay Type: TransRate

Title: TransRate stat on raw tr2aacds transcriptomes

Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: Nonde

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1167.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Created: 7th Nov 2019 at 17:54, Last updated: 16th Nov 2019 at 12:45

_A_02.5_STARlong_matchAnnot

_p_stRT

Assay: A02.5STARlongmatchAnnot

Short Name: 02.5STARlongmatchAnnot

Assay Class: DRY

Assay Type: matchAnnot

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

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

pISA Assay creation date: 2019-10-22

pISA Assay creator: Marko Petek

Phenodata: None

Featuredata: None

...

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1166.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

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

Created: 7th Nov 2019 at 17:50, Last updated: 16th Nov 2019 at 12:55

_A_02.4_STAR

_p_stRT

Assay: A02.4_STAR

Short Name: 02.4_STAR

Assay Class: DRY

Assay Type: STAR

Title: mapping reads back to evigene .tr output

Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map

pISA Assay creation date: 2019-10-22

pISA Assay creator: Marko Petek

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1165.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/samtoolsCoverage.zip, /reports/summaryCounts&SJ.xlsx, /scripts/STAR_commands.txt

Created: 7th Nov 2019 at 17:48, Last updated: 2nd Jun 2020 at 15:42

_A_02.3_InterProScan

_p_stRT

Assay: A02.3_InterProScan

Short Name: 02.3_InterProScan

Assay Class: DRY

Assay Type: InterProScan

Title: InterProScan on tr2aacds output

Description: InterProScan on tr2aacds output

pISA Assay creation date: 2019-10-22

pISA Assay creator: Marko Petek

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1164.1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate/intermediate.tar, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd

Created: 7th Nov 2019 at 17:46, Last updated: 16th Nov 2019 at 13:35

_A_01_evigene

_p_stRT

Assay: A01_evigene

Short Name: 01_evigene

Assay Class: DRY

Assay Type: evigene

Title: EvidentialGene tr2aacds.pl VERSION 2016.07.11

Description: See http://eugenes.org/EvidentialGene/about/EvidentialGenetrassemblypipe.html

pISA Assay creation date: 2019-10-22

pISA Assay creator: Maja Zagorscak

Phenodata: None

Featuredata: None

Data: see ./input/pathtofiles.txt

Submitter: Maja Zagorscak

Biological problem addressed: Integration

Snapshots: Snapshot 1

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_Rywal.tar.gz, /output/output.tar, /scripts/01_run_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh

Created: 7th Nov 2019 at 16:54, Last updated: 16th Nov 2019 at 14:21

Conversion Script for Model Building from KEGG-Reactome Data to SBTOOLBOX2

COSMIC

automated integration of transcriptomic and reactome data to differential equations
structure of the paths is maintained
continuous fermentation model in standard format for data integration, two component model (cell and fermenter)

call >> Kegg2SBToolbox2('modelmap.txt', 'reactionscompounds_final.csv','extracellular.txt','testmodel.txt') for an example

where

model_map is the desired mapping of species,

reactioncompoundsfinal.csv is the entire network,

extracellular.txt is a manual

...

Creator: Sebastian Curth

Submitter: Sebastian Curth

Investigations: Modular Model Building

Studies: Automated Model Building

Assays: Example for model derivation from KEGG

Created: 11th Dec 2012 at 12:43, Last updated: 11th Dec 2012 at 14:39

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

_p_stRT

(Show All)

Abstract (Expand)

Background: Although the reference genome of Solanum tuberosum group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid group … Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research and its subsequent applications in breeding. Results: For the DM genome assembly, two only partially-overlapping gene models exist differing in a unique set of genes and intron/exon structure predictions. First step was to merge and manually curate the merged gene model, creating a union of genes in Phureja scaffold. We next compiled available RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using CLC, Trinity, Velvet, and rnaSPAdes de novo assemblers using different settings to test for optimal outcome. In addition, for cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. Revised EvidentialGene redundancy-reducing pipeline was employed to produce accurate and complete cultivar-specific transcriptomes from assemblers output, as well as to attain the pan-transcriptome. Due to being the most diverse dataset in terms of tissues (stem, seedlings and roots) and experimental conditions, cv. Désirée was the most complete transcriptome (95.8% BUSCO completeness). For cv. Rywal and breeding clone PW363 data were available for leaf samples only and the resulting transcriptomes were less complete than cv. Désirée (89.8% and 89.3% BUSCO completeness, respectively). Cross comparison of these cultivar-specific transcriptomes and merged DM gene model suggests that the core potato transcriptome is comprised of 16,339 genes. The pan-transcriptome contains a total of 95,779 transcripts, of which 54,614 transcripts are not present in the Phureja genome. These represent the variants of the novel genes found in the potato pan-genome. Conclusions: Our analysis shows that the available gene model of double-monoploid potato from group Phureja is, to some degree, not complete. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput -omics analyses, and future breeding programmes.

Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden

Date Published: No date defined

Publication Type: Not specified

DOI: 10.1101/845818

Citation: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Created: 19th Nov 2019 at 12:48, Last updated: 19th Nov 2019 at 12:57