Hello,
I am reading through the Supplementary Methods for CuffDiff 2.
In section 1, it says lt + m - 1 is the effective length of a transcript. In formula 1.1, lt - m + 1 also appears. Later, it is said "... effective length of ... transcripts ... is one, which is the case when the fragments are always the same length as the transcripts being sequenced." It implies that lt + m - 1 is wrong, and that lt - m + 1 is the correct formula.
In formula 1.2, the fold change is simply the ratio of the number of fragments between conditions. How could the condition-specific normalisation term for library size be removed ? It is not a static feature, like effective transcript length is.
I am reading through the Supplementary Methods for CuffDiff 2.
In section 1, it says lt + m - 1 is the effective length of a transcript. In formula 1.1, lt - m + 1 also appears. Later, it is said "... effective length of ... transcripts ... is one, which is the case when the fragments are always the same length as the transcripts being sequenced." It implies that lt + m - 1 is wrong, and that lt - m + 1 is the correct formula.
In formula 1.2, the fold change is simply the ratio of the number of fragments between conditions. How could the condition-specific normalisation term for library size be removed ? It is not a static feature, like effective transcript length is.