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  • arkal
    replied
    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!

    Leave a comment:


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

    Cheers

    Kath

    Leave a comment:


  • arkal
    replied
    bump

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  • arkal
    replied
    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?

    Leave a comment:


  • JackieBadger
    replied
    this may help http://www.bioinformatics.babraham.a.../fastq_screen/

    Leave a comment:


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

    Leave a comment:


  • arkal
    started a topic Contamination in my sample?

    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!

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