I have an exome capture data set for wheat which is hexaploid. I have mapped and called SNPs. The PI wants:
1) A plot of GC content of exons vs read coverage
2) A plot of exon length vs read coverage
3) A figure for the number (%) of reads mapped to exons
4) unique % mapped
5) total % mapped
I can do 4 and 5 but think I'm going to struggle with 1-3. Any ideas (and example commands would be useful) of how to get stats and plot for these qualities, using available tools?