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  • "N"s in DNA sequence data

    I found there're many "N"s in a initial DNA genome sequence data, like:

    CTGAAATCACTACTTTCCTTGTTAGGCTCGGCGCATGTGTTAAGTAGNNN
    NTTATANNCNGNNNAGNATTTATNNNNNNNNCTTNNNNNNCGGTTATATG

    What's the explanation for it? I took BLASTX allignment, no error messages popped up, then how BLAST treats them? Thanks.

  • #2
    Hi rdu

    I see these messy N's always in the Illumina data. I think it could mean variety of different things but this is just my interpretation. Mianly I think when the base caller is not able to decipher which nucleotide to call it leaves "N" behind. If you see bunch of N a the end it could relate to falling quality. However if you see a long stretch in the middle, it could also mean complexity in that genomic region.

    HTH
    -Abhi

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    • #3
      Hi apratap,

      Thank you. Your anwser sounds reasonable. If I know some related futher, will also share with you. Have a nice day.

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      • #4
        Hello,

        The Blast ignore that sequences, there is a lower-complexity filter by default on BLAST to avoid miss-called bases or masked bases (normally N or X correspondingly). You can turn-off that parameter if you want.

        Best regards,
        André.

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