Hi All,
i need to check miRNA differential expression between two 454 run lanes. For this, i summed up all the reads that aligned to each miRNA. and i now have 2 tables that specify each miRNA and the number of reads that aligned to it.
Obviously a normalization needs to be done when comparing these two tables. my question is: normalization to what? should i use the total number of reads (mapped and unmapped) produced from each lane? or should i use the number of mapped reads? or the number of uniquely mapped reads?
i need to check miRNA differential expression between two 454 run lanes. For this, i summed up all the reads that aligned to each miRNA. and i now have 2 tables that specify each miRNA and the number of reads that aligned to it.
Obviously a normalization needs to be done when comparing these two tables. my question is: normalization to what? should i use the total number of reads (mapped and unmapped) produced from each lane? or should i use the number of mapped reads? or the number of uniquely mapped reads?
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