gene_prediction_framework
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| gene_prediction_framework [2022/12/13 14:56] – 129.173.89.83 | gene_prediction_framework [2022/12/13 15:49] (current) – jason | ||
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| + | **This page is now deprecated, check out** [[gene_prediction_with_braker2_pipeline|Gene prediction with Braker2 pipeline]] | ||
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| ===== Gene prediction with Braker2 pipeline ===== | ===== Gene prediction with Braker2 pipeline ===== | ||
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| mv gm_key_64 .gm_key | mv gm_key_64 .gm_key | ||
| - | ===== Repeat masking | + | ==== Repeat masking ==== |
| Mask the repetitive regions in your assembly using the following shell script. BuildDatabase and RepeatModeler will create a species-specific library of repeats from your genome, and then RepeatMasker will use that library to mask repetitive regions in your assembly. | Mask the repetitive regions in your assembly using the following shell script. BuildDatabase and RepeatModeler will create a species-specific library of repeats from your genome, and then RepeatMasker will use that library to mask repetitive regions in your assembly. | ||
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| </ | </ | ||
| - | ===== RNAseq mapping | + | ==== RNAseq mapping ==== |
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| </ | </ | ||
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| - | ===== Genome-guided transcriptome assembly | + | ==== Genome-guided transcriptome assembly ==== |
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| - | ===== Gene prediction with Braker2 | + | ==== Braker2 ==== |
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| - | ===== Predicting gene models with PASA ===== | + | ==== Predicting gene models with PASA ==== |
| PASA will use the genome-guided transcriptome assembly to estimate where gene models are located. It does this by aligning the assembled transcripts to the reference genome. | PASA will use the genome-guided transcriptome assembly to estimate where gene models are located. It does this by aligning the assembled transcripts to the reference genome. | ||
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| </ | </ | ||
| - | ===== Compiling the final gene models with EvidenceModeler | + | ==== Compiling the final gene models with EvidenceModeler ==== |
gene_prediction_framework.1670957803.txt.gz · Last modified: by 129.173.89.83