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  • Contamination in my sample?

    Hi all!

    I just ran a 100bp PE human exome seq run in my lab and was looking at the fastqc results of my run. I am getting this weird pattern in the gc content distribution and was wondering is this normal for an exome run or do i have some sort of contamination? I've run an exome seq before in my lab but saw a distribution which was similar to the theoretical distribution with a shorter peak (yet, still normally distributed). The 2 peaks i'm seeing in the new run is really messing with my head as i have 24 samples all showing the same pattern!

    Thanks in advance!

  • #2
    i don't know why the image is not being shown in the post... here's the link

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    • #3
      this may help http://www.bioinformatics.babraham.a.../fastq_screen/

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      • #4
        Originally posted by JackieBadger View Post
        so i tried this with a couple of my samples vs human.... i'm getting only 3% not mapping. So there is either very little or no contamination in my sample. So then what can explain the bimodal gc content distro?

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        • #5
          bump

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          • #6
            I've just got exactly the same with my data. What kit did you use for capture?

            Cheers

            Kath

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            • #7
              Originally posted by Kath View Post
              I've just got exactly the same with my data. What kit did you use for capture?

              Cheers

              Kath
              TruSeq exome capture.... FYI we saw it in rna seq data also!

              Comment

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