how to analyze the distribution over each gene in different conditions?

Question

[Lila M]

Hi guys, I'm working with gene-exoresion-coverage. Let's say that I have a data frame (49 obs, 4 vars) for each gene (gene), 3 diferent conditions (cond1, cond2, cond3) and coverage as follow:

cond1   cond2   cond3   gene
 418.7  227.7   352.3   SSU72
 32.3   25.3    18.3    TAF5L
 10.7   25.6    36.7    DPYD
 228    219.1   253.3   KIF1B

I would like to analyze the coverage and the distribution of the ratios over each gene in the three conditions. What is the best approach for doing that? Any suggestions?

Thanks!!!

[h.mon]

I guess you are interested in differential gene expression? If yes, you may read limma / edgeR / DESeq2 user guides.

To get more help than the above, explain properly your data and experimental design. How many replicates per condition? Are these RNAseq read counts? ChIPseq? Among other details.

[Lila M]

Hi, thanks for the reply. I'll do the corresponding analysis using the tools that you mentioned. But now I am interested in the coverage over specific genes. So what I want to do is a analysis that, based on my data, could show the distribution for each gene in the different condition. Is not expression data, is coverage. So what I am wondering is which is the best way to show the different distribution for each gene.

Thanks

[h.mon]

If your data is RNAseq, the coverage of a gene will be its expression.

[Lila M]

No, it is not, because I get the coverage using bedtools multicov.