gene_prediction_framework
Differences
This shows you the differences between two versions of the page.
| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| gene_prediction_framework [2022/12/13 14:56] – 129.173.89.83 | gene_prediction_framework [2022/12/13 15:49] (current) – jason | ||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ==== Gene prediction with Braker2 pipeline ==== | + | **This page is now deprecated, check out** [[gene_prediction_with_braker2_pipeline|Gene prediction with Braker2 pipeline]] |
| + | |||
| + | ===== Gene prediction with Braker2 pipeline | ||
| GP using machine learning and extrinsic hints by **DE Salas-Leiva** (last updated Oct-21-2020)\\ | GP using machine learning and extrinsic hints by **DE Salas-Leiva** (last updated Oct-21-2020)\\ | ||
| Line 24: | Line 26: | ||
| 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. | ||
| Line 71: | Line 73: | ||
| </ | </ | ||
| - | ===== RNAseq mapping | + | ==== RNAseq mapping ==== |
| Line 97: | Line 99: | ||
| </ | </ | ||
| | | ||
| - | ===== Genome-guided transcriptome assembly | + | ==== Genome-guided transcriptome assembly ==== |
| Line 122: | Line 124: | ||
| - | ===== Gene prediction with Braker2 | + | ==== Braker2 ==== |
| Line 152: | Line 154: | ||
| - | ===== 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. | ||
| Line 206: | Line 208: | ||
| </ | </ | ||
| - | ===== Compiling the final gene models with EvidenceModeler | + | ==== Compiling the final gene models with EvidenceModeler ==== |
gene_prediction_framework.1670957780.txt.gz · Last modified: by 129.173.89.83