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  • Nucleotide distribution useful?

    I am doing some QC on my illumina sequencing raw data. One of the test I saw other people ran is to do a nucleotide distribution calculation. Is this really some useful information? How do I use it.

    Thanks

  • #2
    Perhaps download the FastQC package to explore your read statistics with a simpel GUI: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

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    • #3
      Yes the nucleotide distribution is useful.

      If the distribution seems "uneven" at the beginning, that could indicate some residual adaptor sequences. The unevenness should be obvious when you compute the distributions of each base.
      SpliceMap: De novo detection of splice junctions from RNA-seq
      Download SpliceMap Comment here

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