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Question: How PacBio quality is calculated?
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gravatar for Medhat
6.3 years ago by
Medhat ♦ 8.8k
Texas
Medhat ♦ 8.8k wrote:

As the question declares I want to know how pacbio quality is calculated?

If I am using the SMRT portal for example RS_Subreads.1

In the filtering process  It will give me this values

SFilter v1

Minimum Subread Length  50

Minimum Polymerase Read Quality  75 

Minimum Polymerase Read Length  50

 

I can change It but how it is calculated?

 

I know that there is two basic steps the Basic analysis step which  begins with movie -> puls -> kinetic measures -> and at last bases

the second step which is called secondary analysis, using the smrt portal which I can change the numbers in each algorithm but how it is related to the main sequences?   

Thanks,
sequencing pacbio alignment • 3.2k views
ADD COMMENT • link •
modified 6.3 years ago by rhall • 160 • written 6.3 years ago by Medhat ♦ 8.8k
2
gravatar for rhall
6.3 years ago by
rhall • 160
United States
rhall • 160 wrote:

In a polymerase (raw) read each base has a set of QVs based on the probability of that base being incorrectly called when calculating base calls from pulses. These QVs include probability of substitution, deletion, insertion and pulse merging. The polymerase read quality is calculated as an estimation of error from the set of QV values for each base in the read. The read quality estimation is conservative, you can see this by comparing the RQ distribution to the mapped accuracy distribution for a known sample.

 
ADD COMMENT • link written 6.3 years ago by rhall • 160

The definition is great. But it doesn't explain clearly how to calculate this QVs using a bam file obtained by mapping reads against the consensus using balsr and/or hisat2 for example ? Are there a list of tools to use to do such a calculation Thank you in advance Best Philippe

ADD REPLY • link written 2.0 years ago by philippe.leroy.2 • 0
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