Genes

Genes that lack expression

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks
Program, Pipeline or Method version: 
Mikado 1.24
Source Name: 
Masonbrink
Time Executed: 
04/16/2021
Materials & Methods (Description and/or Program Settings): 
These are genes that did not have more than 1 unique read mapping from Gardner et al 2017's RNA-seq dataset -- SRX3339090- SRX3339098
Category: 
Default Track?: 

Repetitive Genes that overlap repeatmasker

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks
Program, Pipeline or Method version: 
Mikado 1.24
Source Name: 
Masonbrink
Time Executed: 
04/16/2021
Materials & Methods (Description and/or Program Settings): 
These are genes that were in the original prediction of genes, yet these genes had a 30% overlap with a Repeatmasker repeat, in at least two CDS sequences.
Category: 
Default Track?: 

Genes with transposon annotations

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks
Program, Pipeline or Method version: 
Mikado 1.24
Source Name: 
Masonbrink
Time Executed: 
04/16/2021
Materials & Methods (Description and/or Program Settings): 
These are genes that had reasonable good models, but when functionally annotated they had some form of "transposon", "helitron", or "transposase" in the proteins definition.
Category: 
Default Track?: 

TN10 H.glycines Pseudomolecule Gene Annotation

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks
Program, Pipeline or Method version: 
Mikado 1.24
Source Name: 
Masonbrink
Time Executed: 
03/12/2021
Materials & Methods (Description and/or Program Settings): 
If this information is helpful for your research, please cite the preprint for now. https://www.authorea.com/doi/full/10.22541/au.161538368.83631935/v1 Rick Masonbrink, Tom Maier, Matthew Hudson, et al. A chromosomal assembly of the soybean cyst nematode genome. Authorea. March 10, 2021.
Category: 
Default Track?: 

Genomethreader Alignment of X12 Annotation

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
Genomethreader of Published Annotation
Program, Pipeline or Method version: 
(GenomeThreader) 1.7.1
Source Name: 
Liam et al Gene Models, Masonbrink alignment
Time Executed: 
12/11/2020
Materials & Methods (Description and/or Program Settings): 
(GenomeThreader) 1.7.1
Category: 
Default Track?: 

Genomethreader Alignment of OP50 Braker2 Annotation

Organism: 
Heterodera glycines tn10 private (Soybean Cyst Nematode (tn10) private)
Program, Pipeline Name or Method Name: 
Genomethreader and Braker2
Program, Pipeline or Method version: 
N/A
Source Name: 
Hudson/Showmaker Prediction, Masonbrink Alignment
Time Executed: 
12/11/2020
Materials & Methods (Description and/or Program Settings): 
(GenomeThreader) 1.7.1 Braker 2
Category: 
Default Track?: 

Genomethreader Alignment of TN22 Braker2 Annotation

Organism: 
Heterodera glycines tn10 private (Soybean Cyst Nematode (tn10) private)
Program, Pipeline Name or Method Name: 
Genomethreader and Braker2
Program, Pipeline or Method version: 
N/A
Source Name: 
Hudson/Showmaker Prediction, Masonbrink Alignment
Time Executed: 
12/11/2020
Materials & Methods (Description and/or Program Settings): 
(GenomeThreader) 1.7.1 Braker 2
Category: 
Default Track?: 

Genomethreader Alignment of TN20 Braker2 Annotation

Organism: 
Heterodera glycines tn10 private (Soybean Cyst Nematode (tn10) private)
Program, Pipeline Name or Method Name: 
Genomethreader and Braker2
Program, Pipeline or Method version: 
N/A
Source Name: 
Hudson/Showmaker Prediction, Masonbrink Alignment
Time Executed: 
12/11/2020
Materials & Methods (Description and/or Program Settings): 
(GenomeThreader) 1.7.1 Braker2
Category: 
Default Track?: 

Genomethreader Alignment of TN7 Braker2 Annotation

Organism: 
Heterodera glycines tn10 private (Soybean Cyst Nematode (tn10) private)
Program, Pipeline Name or Method Name: 
Genomethreader and Braker2
Program, Pipeline or Method version: 
N/A
Source Name: 
Hudson/Showmaker Prediction, Masonbrink Alignment
Time Executed: 
12/11/2020
Materials & Methods (Description and/or Program Settings): 
(GenomeThreader) 1.7.1 Braker 2
Category: 
Default Track?: 

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