Normalized coverage histograms for selected chromosome region

Question

[biotech]

I would like to plot the coverage of a genomic region of interest. I'm working with RNA-seq data and my objective is to show an histogram of coverage of a selected region.

I've seen some posts suggesting some tools but none of them seem to be taking normalization into account:

samtools mpileup
samtools depth
bedtools coverage
bedtools genomecov
bedtools multicov
bamtools coverage

Thanks, Bernardo

[biotech]

'-scale' option (Scaling coverage by a constant factor) of bedtools could be an option.

Answer 1

[Devon Ryan]

You presumably already have the normalized values (if not, that's the first thing you need to do), so just plot them with R.

[biotech]

I analized the data using edgeR. I have the normalized values BUT per feature, not per nt (what I really need).

[Devon Ryan]

(1) Scaling the output of any of the tools you listed should work.

(2) Don't read much into small differences, they're likely meaningless unless you have a complete drop in coverage in one group vs. another (and even then, something like DEXseq might be more worthwhile if you just add these regions to your annotation).

[biotech]

(2) Thanks for the comment. I'm interested in up-regulated membrane-related genes for vaccine development. Large fold changes (log2FC>2) are great.