Hello,
I have a question in regarding Illumina quality scores. Which quality control is more reliable: FastQC or the Illumina Sample Summary Information from the Illumina pipeline?
Here is why I ask:
I just get my sequencing data back (from a Hiseq 2000 machine, 50 base run). Based on the Illumina Sample Summary/Report, the quality of the my dataset is decent. The Illumina Sample Summary Information tells me that: The Mean Quality SCore (PF) is 28.43, and %>Q30 bases (PF) is 69.53.
However, when I run my data through FastQC, it tells me that the quality of my data is really really bad (please see the attached images). If you look at the two plots attached, the Mean Quality Score is much much worse than 28.43.
Why is there a discrepancy between the two quality reports? Which one should I believe?
Also, this is the first time our High-throughput Sequencing facility uses the new Illumina pipeline, CASAVA v1.8. I know in the new pipeline the Quality Scores are different from the old one. Could this change explain why FastQC (on Galaxy (version 0.10.0)) thinks my data is poor quality?
Thank you in advance for your help!
-Eric
I have a question in regarding Illumina quality scores. Which quality control is more reliable: FastQC or the Illumina Sample Summary Information from the Illumina pipeline?
Here is why I ask:
I just get my sequencing data back (from a Hiseq 2000 machine, 50 base run). Based on the Illumina Sample Summary/Report, the quality of the my dataset is decent. The Illumina Sample Summary Information tells me that: The Mean Quality SCore (PF) is 28.43, and %>Q30 bases (PF) is 69.53.
However, when I run my data through FastQC, it tells me that the quality of my data is really really bad (please see the attached images). If you look at the two plots attached, the Mean Quality Score is much much worse than 28.43.
Why is there a discrepancy between the two quality reports? Which one should I believe?
Also, this is the first time our High-throughput Sequencing facility uses the new Illumina pipeline, CASAVA v1.8. I know in the new pipeline the Quality Scores are different from the old one. Could this change explain why FastQC (on Galaxy (version 0.10.0)) thinks my data is poor quality?
Thank you in advance for your help!
-Eric
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