discordant results between bedTools and awk
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Entering edit mode
5.8 years ago
bioguy24 ▴ 220

The output from the bedTools 2.17 command below:

coverageBed -abam IonXpress_009_150603.bam -b epilepsy70_medex.bed -counts > count.txt

and this awk

awk '{if(len==0){last=$4;total=$6;len=1;getline}if($4!=last){printf("%s\t%f\n", last, total/len);last=$4;total=$6;len=1}else{total+=$6;len+=1}}END{printf("%s\t%f\n", last, total/len)}' output.bam.hist.txt > epilepsy70_average.txt

are different though, I believe, they are both calculating the average read depth per target in the bed file.

Count.txt

chr1    40539722    40539865    chr1:40539722-40539865    281
chr1    40542489    40542609    chr1:40542489-40542609    126
chr1    40544221    40544341    chr1:40544221-40544341    77

epilepsy70_average.txt

chr1:40539722-40539865    227.776224
chr1:40542489-40542609    104.300000
chr1:40544221-40544341    61.54166

I do not see a way to attach but the awk basically uses the output of:

coverageBed -hist -d -abam IonXpress_001.bam -b LCH_IDT > output.bam.hist.txt

​and combines and averages all baits that match.  Why are the outputs different?

Thank you :).

 

 
next-gen bedtools awk • 1.3k views
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Entering edit mode

The bedtools coverage command does not calculate the average read depth, it calculates how many reads align to / overlap a region.

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