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Old 08-23-2011, 10:43 PM   #1
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Location: Canada

Join Date: Aug 2011
Posts: 3
Default effect of mRNA contamination

We have sequenced some yeast strains with very high coverage (~30x). However, seems like our samples were contaminated with mRNA. Seems like we have much more coverage at coding sites. Before doing any downstream analysis, I would like to know what kind of (hidden)side effects would this cause in terms of (a) coding snp calling, (b) non-coding snp calling, and (c) de-novo assemly and structural variant calling ? Do you guys think it is garbage and we should re-sequence or we might still do something with it?
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