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After assembling some reads using Velvet-Oases, I noticed that many occasions, the 5' of a CDS would be missing. Sometimes, its the 3' end that is missing but mostly the 5'. Is this due to the degradation of mRNA before/during the sequencing process?
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We need to know some details about library construction to answer with any certainty. But the issue you are most likely seeing is that the library is the result of the poly A-based isolation of mRNA from total RNA. Because the poly A tail is at the 3' end of the mRNA, any degradation of the RNA sample will cause the 5' end of the message to be lost.
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Phillip
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