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gene_prediction_with_braker2_pipeline [2025/11/18 12:17] – [Braker2] 134.190.191.148gene_prediction_with_braker2_pipeline [2025/11/18 14:23] (current) – [Genome-guided transcriptome assembly] 134.190.191.148
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 #$ -cwd #$ -cwd
 #$ -pe threaded 10 #$ -pe threaded 10
 +
 cd $PWD cd $PWD
 +
 source activate trinity-2.11-with-workaround source activate trinity-2.11-with-workaround
-Trinity --CPU 10 --max_memory 100G --genome_guided_bam yourgenome.fasta.sambamsorted.bam --genome_guided_max_intron 1000 --SS_lib_type RF+ 
 +Trinity \ 
 +    --CPU 10 \ 
 +    --max_memory 100G \ 
 +    --genome_guided_bam yourgenome.fasta.sambamsorted.bam \ 
 +    --genome_guided_max_intron 1000 \ 
 +    --SS_lib_type RF 
 conda deactivate conda deactivate
 </code> </code>
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 [[https://github.com/Gaius-Augustus/BRAKER|Braker]] is a fully automated pipeline in which [[https://github.com/Gaius-Augustus/BRAKER|Braker]] is a fully automated pipeline in which
  
-  - 1. Intron start and end coordinates (//intron hints//) are extracted from the RNAseq BAM file +  - Intron start and end coordinates (//intron hints//) are extracted from the RNAseq BAM file 
-  - 2. These are then used along with the genome FASTA file to train GeneMarkET +  - These are then used along with the genome FASTA file to train GeneMarkET 
-  - 3. The trained GeneMarkET performs an "//ab initio//" gene prediction +  - The trained GeneMarkET performs an "//ab initio//" gene prediction 
-  - 4. Those predicted gene structures for which all introns are supported by the RNAseq data (//anchored introns//) are selected to train AUGUSTUS +  - Those predicted gene structures for which all introns are supported by the RNAseq data (//anchored introns//) are selected to train AUGUSTUS 
-  - 5. The trained AUGUSTUS now predicts gene structures using again the intron hints as "extrinsic evidence"+  - The trained AUGUSTUS now predicts gene structures using again the intron hints as "extrinsic evidence"
  
 {{::braker1_pipeline.png|}} {{::braker1_pipeline.png|}}
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 If you only use RNAseq as extrinsic evidence, you essentially can only use //donor splice site// and //acceptor splice site// hints. If you also have protein homology information, you can also infer and use //start//, //stop//, //exonpart// and //exon// hints (Stanke et al 2006) If you only use RNAseq as extrinsic evidence, you essentially can only use //donor splice site// and //acceptor splice site// hints. If you also have protein homology information, you can also infer and use //start//, //stop//, //exonpart// and //exon// hints (Stanke et al 2006)
  
 +The intron hints contain explicit location information and influence the optimal path through the GHMM machine (AUGUSTUS+ paper, Stanke et al 2006). It is important to note that since this is a probabilistic model, **hints can sometimes be ignored if the intrinsic information is strong enough!**
  
 Predict genes using Genemark-ET and Augustus through braker2: Predict genes using Genemark-ET and Augustus through braker2:
gene_prediction_with_braker2_pipeline.1763482674.txt.gz · Last modified: by 134.190.191.148