Yaamini’s Notebook: Gonad Methylation Analysis Part 4

Preparing a genome (and my brain)

I forgot just how time-consuming (and brain pain-inducing) bioinformatics pipelines are! Good thing I set up my monitor. Screensharing on my laptop screen would not be ideal.

I created a new Jupyter notebook for the Bismark portion of my pipeline. Here’s the basic outline of the Bismark pipeline:

  1. Genome preparation
  2. Alignment
  3. Methylation extraction
  4. HTML report
  5. Summary report

I got started on the genome preparation portion. To do this, I first downloaded the genome from NCBI. I learned that when you download FASTA files from NCBI, it specifies what kind of FASTA it is. In my case, I downloaded a .fna, or nucleotide FASTA file for the genome. I had to convert the .fna to an .fa for Bismark using the handy cp command.

Obviously I needed Bismark and Bowtie2 on the Mac mini before I could use it. This part was obviously strugglesome (see this issue if you don’t believe me). I downloaded Bismark from this website, and Bowtie2 using this code:

conda install -c bioconda bowtie2

It was simple, but Steven suggested downloading the source code in the future to have more control over versioning and the full path.

Finally, I could use the bismark-genome-preparation command. Here’s what I needed:

  1. Path to bismark-genome-preparation
  2. –path-to-bowtie + the path to the folder with bowtie2, and not the path to bowtie2
  3. –verbose, which prints detailed status reports
  4. Path to the folder with the .fa or .fasta genome file

And it’s running! I’ll check on it later tonight to see if I can move on to the alignment step.

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