Has anyone done more than a perfunctory analysis of unmapped reads in SOLiD and Illumina data?
I did a quick alignment against UCSC's unassembled data and found that the most amount of originally unmapped reads map to mitochondrial DNA. However, at most this was ~1% of the originally unmapped reads.
I suspect that much of the unmapped reads are artifacts such as PCR dimers and self ligated oligos (for SOLiD). If it is, there may be easy molecular protocol steps to remove them.
I did a quick alignment against UCSC's unassembled data and found that the most amount of originally unmapped reads map to mitochondrial DNA. However, at most this was ~1% of the originally unmapped reads.
I suspect that much of the unmapped reads are artifacts such as PCR dimers and self ligated oligos (for SOLiD). If it is, there may be easy molecular protocol steps to remove them.
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