I'm interested in checking the conservation of lncRNAs and protein-coding genes from Gencode and similarly from my data I also have some newly assembled lncRNAs which are not found in gencode. I would like to make a plot like below:
The above image is taken from the paper Recurrently deregulated lncRNAs in hepatocellular carcinoma. Figure 1e
Similar to above image, I also wanted to check the conservation of known lncRNAs, protein coding genes and newly found lncRNAs.
How to calculate the phastcons score for all the genes?