Hi, I have 10 bam files with many contigs.
I created bed files for each one (with bedtools genomecov)
How can I create a histogram that shows coverage depth (In the x-axis) and the number of bases in the genome (In the y-axis) ? One histogram for each bam file.
like this:
Thanks!
•
written
by
Michal Nevo •
You can use deepTools' plotCoverage tool, which will generate 2 slightly different plots, but will allow you to extract the table of counts that you can use to generate a histogram in any other tool of your liking, e.g. via R
Details are here
Can you explain? I've already created these 2 graphs..but this is not what I need. I'm looking for a way to create the graph I need.
Did you mean I should create this file?
I already have a coverage file.
correct, the --outRawCounts option will generate a file where each row corresponds to the number of reads found at a given bp position.
Here's the example code from the deepTools documentation:
$ head coverage.tab
'H3K27me3' 'H3K4me1' 'H3K4me3' 'H3K9me3'
0 0 0 0
0 0 0 0
0 0 0 0
0 0 0 0
0 0 0 0
0 0 0 0
0 0 0 0
0 0 0 0
0 0 0 0
$ cut -f1 coverage.tab | sort -n | uniq -c
1 'H3K27me3'
548190 0 # the vast majority of sampled bp had 0 overlapping reads
127914 1
35703 2
12271 3
4584 4
1717 5
659 6
251 7
106 8
49 9
16 10
6 11
3 12
2 13
3 14
1 15
1 16
2 17
1 19
1 21
2 22
1 23
1 24
2 28
1 35
1 40 # there was one bp with 40 overlapping reads!
1 44
uniq -c will return two columns as shown above -- the first one contains the values your example plot has on the y axis ("number of bp in the genome") and the second column contains the coverage value, which is shown on the x axis. In the example above, the peak would be to the far left, i.e. at 0x coverage.
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I guess QualiMap has this option.