Question: Normalized coverage histograms for selected chromosome region
0
gravatar for biotech
4.3 years ago by
biotech510
United States
biotech510 wrote:

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

rna-seq coverage • 2.1k views
ADD COMMENTlink modified 4.3 years ago by Devon Ryan86k • written 4.3 years ago by biotech510

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

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by biotech510
0
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

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

ADD COMMENTlink written 4.3 years ago by Devon Ryan86k

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

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by biotech510

(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).

ADD REPLYlink written 4.3 years ago by Devon Ryan86k

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

ADD REPLYlink written 4.3 years ago by biotech510
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