How many methylation and expression values do you have per gene? If per gene you have a table named - *gene_corr*; which has two columns - *methylation_values* and *expression_values*, then you could indeed just do: corr(gene_corr$methylation_values, gene_corr$expression_values) As a sanity check, if the dimension of *gene_corr* differs per...

I discovered a problem while trying to analyze RNA-seq expression data using DEseq2. DEseq2 is a tool for unnomalized data, that is, raw count, and my data is RPKM data. Since all I have is an expression matrix, I think it's difficult to convert it to a raw count. So, this is a headache. What tool should I use to find the different expression genes...

thx for the explanation. I did look at the function and I also read in the help page, that you get a patchwork object, only when using `combine = TRUE`. I also can't see in the function script, where they look at how many features I input.

Thank you, I'll check out Quast!

Looking at the source code of the function it seems that they make individual plots with ggplot when `features` is `> 1` and then use patchwork to stitch them. Hence, use patchwork functionality to apply standard ggplot manipulations. Standard ggplot would be `plot + theme(plot.title = element_text(size = 40, face = "bold"))` and in patchwork...

Thank you for the response to answer you question, no, the ddRADseq data (short paired end illumina reads) for all the samples were used to generate the query file. the data was clustered (CD-HIT) and assembled to generate a de novo reference genome consisting of multiple contigs, resulting in a FASTA file with contigs resulting from the clustering...