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  • Discovery of viral pathogen from IonTorrent data

    All,

    I'm seeking your advice and suggestions to identify the viral genome from viral-infected patient sample sequenced on IonTorrent. A totol 0.34 million reads of length 5-202bp DNA reads was generated, out of which 0.30 million reads were selected after filtering low quality reads based on read length (<20bp), quality trim (Q<14 at 5', 3') and mean QV <14.

    1) To substract the human background, the remaining reads were mapped to hg19 using Tmap, bwa, Bowtie2 using default params, provided different mapping results 45%, 10%, 12% respectively. But I see Tmap reported mapping even with say 18bp match in 200bp read, probably the reason for high mapping %. But all of them showed only 8-12% mapping with mapQ>8. What;s your opinion on this? Any other aligned I should try or any specific parameters?

    2)Next, I would like to map the unmapped reads to ~4000 viral genome db from NCBI. How can I do this as I would get the % of reads mapped to each genome and get a summary of mapping. Which tool does suite best to this?

    Anyone has any previous experience on this kind of analysis (with IonTorrent data)?

    Thanks

    Raj

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