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
1 answer
You presumably already have the normalized values (if not, that's the first thing you need to do), so just plot them with R.
(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).
Log in to answer this question.
-
How to obtain zero-based coordinates read depth using bedtools coverage for a specific region?
written by vladimiralan •
-
getting a set of coverage/depth metrics for multiple regions
written by vaushev •
-
Calculate scaffold coverage without ambiguous (N) bases
written by ThomasL70 •
-
calculation of coverage for a given region
written by tonja.r
-
How to down-sample a BAM file read depth to reduce heterogeneity in coverage while keeping heterozy…
written by Bruno Vieira •
-
Genomic Coverage - Samtool's undocumented "depth" verses the poorly documented pileup.
written by John
-
R1 R2 orientation (RNA-seq)
written by biotech
-
Snp Density
written by int11ap1
-
Total Number Of Mapped Bases In Exome Ngs Data
written by User6891
-
What Is The Fastest Method To Determine The Number Of Positions In A Bam File With >N Coverage?
written by Malachi Griffith
'-scale' option (Scaling coverage by a constant factor) of bedtools could be an option.