Hi,
I have just received our first Illumina data & I have assembled it into Consed. Then I searched for high quality discrepancies as am looking for variants.
But also in the list brought up it has discrepancies with 'n' (masked) sequence in the RefSeq.
Why would the program compare the sequences to regions of N's . I would have thought it would only be looking for differences between the 4 bases.
How can I screen these out to reduce my long list of discrepancies?
Thanks alig
I have just received our first Illumina data & I have assembled it into Consed. Then I searched for high quality discrepancies as am looking for variants.
But also in the list brought up it has discrepancies with 'n' (masked) sequence in the RefSeq.
Why would the program compare the sequences to regions of N's . I would have thought it would only be looking for differences between the 4 bases.
How can I screen these out to reduce my long list of discrepancies?
Thanks alig
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