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  • @Phil: Is a better fix coming along for this? That kind of seems like a hacky solution.

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    • Originally posted by GenoMax View Post
      @Phil: Is a better fix coming along for this? That kind of seems like a hacky solution.
      No idea You'll have to ask Simon about that..

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      • Hello,

        Does any one know where I can find average Q score on miseq raw reads fastQC report? I know fastQC gives per sequence Q scores. But it doesn't tell the average Q scores of the raw reads though. Thank you very much in advance.

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        • Hi @fnn4,

          Do you mean a single mean quality score for the entire FastQ file? The Per Sequence Quality Scores plot shows the distribution of average Q scores across all reads in the file. I don't think that FastQC reports an average for the entire file, but it should be simple enough to do using the raw data reported in fastqc_data.txt - just sum the (Q score * read count) from the per-sequence section and divide by the sum of the read count.

          What's your reason for wanting this statistic, out of interest?

          Phil

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          • Hi Phil,

            Thank you for your reply. Yes, that is what I was asking for. When we submit samples, we have to pass a certain threshold for average Q score.
            Originally posted by ewels View Post
            Hi @fnn4,

            Do you mean a single mean quality score for the entire FastQ file? The Per Sequence Quality Scores plot shows the distribution of average Q scores across all reads in the file. I don't think that FastQC reports an average for the entire file, but it should be simple enough to do using the raw data reported in fastqc_data.txt - just sum the (Q score * read count) from the per-sequence section and divide by the sum of the read count.

            What's your reason for wanting this statistic, out of interest?

            Phil

            Comment


            • FastQC weird Kmer count in GBS data

              Hi @simonandrews and everybody elese, I'm using FastQC to check the quality of my GBS reads, focusing in th R1 sequences, and I'm getting weird results in the Kmer content. After trimming and removing adapters and barcodes, I got a first Kmer profile showing a higher than expected count for several 6-mers, like this:
              Click image for larger version

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              I thought it may be the adapters of the other side of the read for the sequencing of the R2, so I trimmed all the reads longer than 130 pb to 130 pb. And strangely, I got new Kmer peaks, not shown before:

              Click image for larger version

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              Does anybody know why and what are these new peaks, or what it's the origin of them? May be related with FastQC algorithms? Somebody found similar problems? Thanks a lot guys!!

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              • I most want to say that you are doing a great job.
                Last edited by hiretabletsae; 02-06-2019, 10:07 PM.
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