Dave Carlson davidecarlson

## gene_structure_stats.md

      
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                darencard
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              April 18, 2023 13:35
            
              
                Script to produce estimates of gene structure
              
          
    Please see the most up-to-date version of this protocol on my blog at https://darencard.net/blog/.
Inferring the structure of gene annotations

When annotating genomes it is often desireable to know the overall structure of genes, including information like exon and intron lengths among other metrics. Here is a program genestats that will calculate such measures for a user.
#!/usr/bin/env bash

usage()

  
## maker_genome_annotation.md

      
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              March 7, 2024 08:50
            
              
                In-depth description of running MAKER for genome annotation.
              
          
    Please see the most up-to-date version of this protocol on my blog at https://darencard.net/blog/.
Genome Annotation using MAKER

MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.
Software & Data

Software prerequisites:


RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (ver