Calculate Exome Coverage

[Coryza]

*// Edit to make the post more clear (Mapping done via Bowtie2).
My problem is that when counting Exome Coverage via coverageBed gives different results than via genomeCoverageBed. So I'm not sure if I'm doing something wrong, or which of the 2 methods is correct.

1) My first step is to build an .bed file of my Illumina Paired-End reads, returning the positions that only fall in targeted exon regions. I'm doing that via intersectBed -a [data.bed] -b [illuminaexonregions.bed].

2) My next step is to calculate the coverage of my new datafile via coverageBed -a [newdata.bed] -b [illuminaexonregions.bed]. I calculated some statistics:
Number of exons **214126** with a total length of **45326818**
Number of matched nucleotides **10993449.0**
Nucleotides/Length*100 **24.253740909** % Coverage.

3) The next step was to calculate the coverage of my new datafile via genomeCoverageBed -i [newdata.bed] -g [genome.txt] -d awk '$3>0 {print $1"\t"$2"\t"$3}'. I calculated some statistics:
Number of exons **214126** with a total length of **45326818**
Number of matched nucleotides **10576907.0**
Nucleotides/Length*100 **23.3347661863** % Coverage.

Somehow there's a difference in matched nucleotides, which I can't explain. What am I doing wrong?

[TiborNagy]

coverageBed calculate coverages where the two bed files are overlap.

[Coryza]

True. So when I coverageBed -a [data filtered exon regions] -b [exons] that should give the same result when genomeCoverageBed -i [data filtered exion regions] -g [genome] -d.?

[TiborNagy]

Yes, If everythink is working correctly.

[Baseless]

This will not directly solve your problem, but save you some time: You can run coverageBed directly from the bam file and save the time/IO needed to produce a bed file of the sequencing data first.
I do my coverage checks like this:
coverageBed -abam <final_bam_file> -b <enrichment_kit_track_file> -hist