Plotting Genomic Coordinates

Question

[joe_genome]

Hello,

I'm trying to use the genomicalignments package in r to plot the coordinates of subsampled aligned bam files, these have been sorted and marked already for duplicates.

I want to compare some alignment files from the same sample, I would like to plot a scatterplot to see if there are overlap of reads or the genomic coordinates.

Not sure if this is the way to go.

Still new to bioinformatics/programming :)

Answer 1

[seidel]

Not completely clear to me what you actually want, but if you have imported your BAM files into GenomicAlignment objects, you could convert them to GRanges objects and simply make a scatter plot:

library(GenomicRanges)

sample1_gr <- GRanges(sample1)
sample2_gr <- GRanges(sample2)

# scatter plot of start positions
plot(start(sample1_gr), start(sample2_gr))

# draw the diagonal
abline(0,1)

anything on the diagonal is the same. I highly doubt this is what you want.

# How many overlaps exist between samples?
sum(countOverlaps(sample1_gr, sample2_gr, ignore.strand=TRUE))

What question are you asking of your scatter plot? Maybe how many reads are identical between samples?

# resize to single nucleotide
s1 <- resize(sample1_gr, 1, fix="start")
s2 <- resize(sample2_gr, 1, fix="start")
sum(countOverlaps(s1, s2))

[joe_genome]

Thanks for the response @seidel :) I actually want to know if there is a correspondence on the diagonal, I then want to remove the reads that have a matching start and end to see if there is any type of base shift done during alignment etc. Thanks, this points me in the right direction.