Javan Okendo Jokendo-collab

## maker_genome_annotation.md

      
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                Jokendo-collab
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              November 27, 2022 02:00
                — forked from darencard/maker_genome_annotation.md
            
              
                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 (ve


## STAR.md

      
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                Jokendo-collab
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              April 20, 2019 12:01
                — forked from ipurusho/STAR.md
            
              
                A brief tutorial on how to run the STAR aligner on medinfo.mssm.edu
              
          
    ###Download STAR###
Obtain STAR source from https://github.com/alexdobin/STAR
Add the following to your .bashrc file and source it:
export PATH=/path/to/STAR/bin/:$PATH
###Generate Reference Genome

  
## deinterleave_fastq.sh
#!/bin/bash
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
#
# Deinterleaves a FASTQ file of paired reads into two FASTQ
# files specified on the command line. Optionally GZip compresses the output
# FASTQ files using pigz if the 3rd command line argument is the word "compress"
#
# Can deinterleave 100 million paired reads (200 million total
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
#
	#!/bin/bash
	# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
	#
	# Deinterleaves a FASTQ file of paired reads into two FASTQ
	# files specified on the command line. Optionally GZip compresses the output
	# FASTQ files using pigz if the 3rd command line argument is the word "compress"
	#
	# Can deinterleave 100 million paired reads (200 million total
	# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
	#