Hi Members,
Organism: S. aureus
I've 100 isolates' Illumina WGS. That is 2*100 fastq.gz files. Read length 100.
Unfortunately, the run failed before completing last 6 cycles.
Sequencing centre has de-multiplexed data, and we've it in our court now.
My challenge here is to strike out isolates which have poor quality. I'm interested for R2 only.
One approach I know is:
Get fast-qc report for all the R2, and visually decide(pass,fail) respective data one by one.
Then again that would be qualitative, and thus I do not want to go for this approach (for the time being).
Also, poor is a subjective term.
Let's say, I'd like to have isolates with an average of 25 coverage. Is there way to do so?
I'm sure this situation is very common with other labs.
Looking forward for guidance!
Organism: S. aureus
I've 100 isolates' Illumina WGS. That is 2*100 fastq.gz files. Read length 100.
Unfortunately, the run failed before completing last 6 cycles.
Sequencing centre has de-multiplexed data, and we've it in our court now.
My challenge here is to strike out isolates which have poor quality. I'm interested for R2 only.
One approach I know is:
Get fast-qc report for all the R2, and visually decide(pass,fail) respective data one by one.
Then again that would be qualitative, and thus I do not want to go for this approach (for the time being).
Also, poor is a subjective term.
Let's say, I'd like to have isolates with an average of 25 coverage. Is there way to do so?
I'm sure this situation is very common with other labs.
Looking forward for guidance!
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