I have the assembly file of a certain lizard species, I wanted to recreate Fig. 2 of the following paper, which compares the GC content distribution over 5kb windows, how would I go about doing this?
I would suggest using
bedtools makewindows and
bedtools nuc to compute the GC content for genomic windows as shown in Fig 2 of the linked paper.
See related question here.
This will slice the genome into 5Kbp (or whatever size specified to
makewindows) pieces and compute the GC content of each piece, which can be plotted as a distribution as in the figure.
Something like this would work for the 5000 bp example:
# assemble a bedtools compatible genome file: # see https://www.biostars.org/p/70795/ for hints how to do this. bedtools makewindows -w 5000 -g my_genome.genome > windows.bed # you just made this .genome file manually bedtools nuc -bed windows.bed -fi my_genome.fasta > windows_gc.bed
The bed output file will contain the GC content of each window in the
7_pct_gc column (according to my understanding of the output file).