Hello!
As far as I know, Pacbio sequencing shouldn't have any GC-bias at all, or at least very small.
When I was comparing GC-bias in a couple of samples (using Picard's CollectGcBiasMetrics) sequenced with different technologies I noticed that the Pacbio graph appeared particularly strange: http://i57.tinypic.com/2rxbgc0.png
Basically an inverted normal-distribution rather than a flat line if no bias.
The GC-bias is calculated from a bamfile where the PBcR are aligned using BLASR back to the scaffolds produced in an assembly.
The graphs I produced for other technologies looks more or less as expected.
Anyone know what is going on, or am I doing something terribly wrong?
Something due to the fact that the reads are error-corrected?
As far as I know, Pacbio sequencing shouldn't have any GC-bias at all, or at least very small.
When I was comparing GC-bias in a couple of samples (using Picard's CollectGcBiasMetrics) sequenced with different technologies I noticed that the Pacbio graph appeared particularly strange: http://i57.tinypic.com/2rxbgc0.png
Basically an inverted normal-distribution rather than a flat line if no bias.
The GC-bias is calculated from a bamfile where the PBcR are aligned using BLASR back to the scaffolds produced in an assembly.
The graphs I produced for other technologies looks more or less as expected.
Anyone know what is going on, or am I doing something terribly wrong?
Something due to the fact that the reads are error-corrected?
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