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The command I used:
gene_list=['Psd3', 'Dcx', 'Syt11', 'Ntrk2', 'Gnao1', 'Gria1', 'Dctn3', 'Map1b', 'Camk2a', 'Gpm6b', 'Sez6l', 'Evl', 'Astn1', 'Ank2', 'Klf7', 'Tbc1d16', 'Atp1a3', 'Stxbp6', 'Scn2a…
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Hello, I am new to gene prediction. As part of my research I have to predict the number of genes on some of my scaffolds. For one of my scaffolds (scaffold 10) its size is sufficient for Braker3 to ru…
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Hi Austin,
GMAP is an aligner that do not account for gene functionality (completeness, absence if STOP codons, frame-shift etc.). Just aligning the transcript sequence does not tell anything about…
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Hi, I really like your approach for modelling ordinal data and am trying it on my data. I have gene expression data and ordinal response data as well as categorical unpenalized factors. I have split m…
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Hi,
I am using the calculated data from STAR to infer the cancer type using TULIP.
There are many genes without expression value, and I encountered some mistake after running the command, which …
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How Can I change the length parameter of predicted ORFs. I would like to specify sequences > 15bp, predict sequences larger than this size.
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Hi,
I was running braker3 with etp mode, and get the final braker.gtf file. Compared to the Augustus/augustus.hints.gtf which predicted 68857 genes, the final braker.gtf preserved only 39896 genes.…
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Hello !
I have a question more than an issue, but maybe you can help me,
I am annotating a dozen of arthropods assemblies from a same genus with braker3 (arthropoda prot + RNAseq data),
For a…
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"This resource consists of mouse sperm lines for ENU-induced single-SNV mutations across more than 10,000 genes. In total there are over 250,000 SNVs that have been computationally predicted for effec…
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While executing the ranking logic with **GNNExplainer**, it seems that the function [`predict_candidate_genes_gnn_explainer_only` in file `GDARanking.py`](https://github.com/GiDeCarlo/XGDAG/blob/fdfeb…