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  • Question about the values of quality

    Hi everybody:

    This is my first post here and it will be not the last one .

    After checking some quality values for reads (Solid system) , i saw that most the values are between 2 and 34 and sometime (-1) which corresponds to the dot.
    Anyone have an idea about these values range.

    Thanks in advance.

  • #2

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    • #3
      Your data doesn't sound very high quality. 80% of the quality values should be greater than 30 (max of 40 with the 3Plus)

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      • #4
        The probability of a base being wrong p is given by p = 1/10 ^ QV/10

        (The ^ means 10 to the QV/10 exponential ). Thus a QV of 20 means 1 in 100 chance of being wrong, 30 is 1 in 1000 etc.


        Massively parallel, tag-based sequencing systems, such as the SOLiD system, hold the promise of revolutionizing the study of whole genome gene expression due to the number of data points that can be generated in a simple and cost-effective manner. We describe the development of a 5′–end transcriptome workflow for the SOLiD system and demonstrate the advantages in sensitivity and dynamic range offered by this tag-based application over traditional approaches for the study of whole genome gene expression. 5′-end transcriptome analysis was used to study whole genome gene expression within a colon cancer cell line, HT-29, treated with the DNA methyltransferase inhibitor, 5-aza-2′-deoxycytidine (5Aza). More than 20 million 25-base 5′-end tags were obtained from untreated and 5Aza-treated cells and matched to sequences within the human genome. Seventy three percent of the mapped unique tags were associated with RefSeq cDNA sequences, corresponding to approximately 14,000 different protein-coding genes in this single cell type. The level of expression of these genes ranged from 0.02 to 4,704 transcripts per cell. The sensitivity of a single sequence run of the SOLiD platform was 100–1,000 fold greater than that observed from 5′end SAGE data generated from the analysis of 70,000 tags obtained by Sanger sequencing. The high-resolution 5′end gene expression profiling presented in this study will not only provide novel insight into the transcriptional machinery but should also serve as a basis for a better understanding of cell biology.

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        • #5
          Also, ABI claims that 80% of the QV should be greater than 30. I haven't checked this personally. They do funny things with their statistics like counting only mapped reads. Since only ~70% of the tags typically will map to a reference genome this seems a bit suspicious.

          Illumina does something similar though in that it first filters out poor tags before creating the text data files.

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          • #6
            Got it , thanks a lot for your answers

            Best regards

            Comment

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