unigene assembly for snp calling
I have a generic quetion regarding SNP calling for RNA seq data. Generally, the reference genome should be considered for SNP calling but what if it is not available? In that case, can one use:
the reference transcriptome?
if reference transcriptome is also unavailable, can one use the unigenes compiles in a multifasta as reference for SNP calling?
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lakhujanivijay
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