Download the GENCODE human genome annotation version Release 44 (GRCh38.p14) using the following link: GFF3
Write R code to perform each of the following tasks.
1. Numbers of genes on each chromosome
Visualize using bar plot (function barplot()) the total number of genes on each chromosome (1-22, X, Y). Report the chromosomes with the min and max number of genes.
2. Gene density on each chromosome
Visualize the density of genes on each chromosome. Density is defined by the total number of genes divided by the length of the chromosome. You can use the maximum end coordinate value to approximate the length of a chromosome. Point out the chromosomes with the minimum and maximum gene density, respectively.
3. Numbers and density of transcripts on each chromosome
Repeat 1 and 2 for transcripts.
4. Numbers and density of CDSs on each chromosome
Repeat 1 and 2 for CDS.
5. Overall statistics
5.1 How many intervals are annotated in this version?
5.2 What is the total number of genes annotated in the human genome?
5.3 How many are protein coding genes?
5.4 How many are noncoding genes?
Read more here: Source link