Hi,
a simple task.. or should be. I need to extract the average coverage per feature in a bam file. I have a genbank and bed file for the reference the bam was mapped to. if I map with e.g. Geneous I can see good, variable coverage over the reference genome. I have tried GATK (could not get to run) and Bedtools (genomecov and coverage) -coverage will give me an output file but all the features have zero coverage..
here's the top of the .bed file:
track name="Example E.coli"
o26chr.gb 189 255 thrL gene 0 +
o26chr.gb 189 255 thrL CDS 0 +
o26chr.gb 336 2799 thrA gene 0 +
o26chr.gb 336 2799 thrA CDS 0 +
o26chr.gb 2800 3733 thrB gene 0 +
o26chr.gb 2800 3733 thrB CDS 0 +
o26chr.gb 3733 5020 thrC gene 0 +
o26chr.gb 3733 5020 thrC CDS 0 +
o26chr.gb 5233 5530 yaaX gene 0 +
Here's the top of the output from bedtools coveage -ibam file.bam -b file.bed
o26chr.gb 1047122 1048841 poxB gene 0 - 0 0 1719 0.0000000
o26chr.gb 1047122 1048841 poxB CDS 0 - 0 0 1719 0.0000000
o26chr.gb 2096828 2097287 gene 0 + 0 0 459 0.0000000
o26chr.gb 3144900 3148635 yfaL gene 0 - 0 0 3735 0.0000000
o26chr.gb 3144900 3148635 yfaL CDS 0 - 0 0 3735 0.0000000
o26chr.gb 4194149 4194368 tdcR gene 0 + 0 0 219 0.00 ...
↧