<aside> 💡 wiggle or wig files are files that store some kind of signal (usually just a number) associated with a nucleotide.

To visualise and thus load wig files into JBrowse (genome browser), you need to convert them to bigWig first.

Here I show how to convert wig to bigwig using the command line tool wigToBigWig.

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Requirements

• Download and install wigToBigWig: http://hgdownload.cse.ucsc.edu/admin/exe/
• A .wig file that you want to convert

Steps

1. Prepare your chrom.sizes file which lists the sizes of all chromosomes. The file will look like this:

   cat chrom.sizes
   
   I	230218
   II	813184
   III	316620
   ...
   

   1. Create a fasta index from the fasta file that your wiggle file is associated with:

      samtools faidx <example.fasta>
      

      This creates a .fai file which is your index file.

   2. Cut that index down to only contain the chrom sizes

      cut -f1,2 <example.fai> > chrom.sizes
      

2. Now, run wigToBigWig:

wigToBigWig <in.wig> <chrom.sizes> <out.bw>