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Update 5. Annotation.md
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sahoo-rk authored Jul 15, 2024
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Expand Up @@ -99,7 +99,7 @@ Assessing the gene annotation by checking the identified CDS regions against the
```bash
# Annotation quality assessment
busco -i ~/path/to/dir/in/braker.codingseq --out_path ~/path/to/dir/out -o $prefix -l ~/path/to/dir/out/$busco.db \
-m protein --offline -c $threads --augustus_parameters='--progress=true' --download_path ./busco_downloads
-m protein --offline -c $threads --augustus_parameters='--progress=true' --download_path ~/path/to/dir/in/busco_downloads
```
Checking the annotations to find if there exist any potential overlap among the repeat regions (output from RepeatMasker) and the protein-coding regions (BRAKER output).
```bash
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