how does cufflinks caculate the expression
i want to know which formula cufflinks uses to caculate the expression and p-value. in my .bam file, some transcripts have reads mapped, but don't have expression when caculated by cufflinks
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This is the cufflinks paper - it has formulae for expression calculation:
Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Nature Biotechnology doi:10.1038/nbt.1621
In particular, read 'Transcript abundance estimation' in Methods section and '3. Transcript abundance estimation' in Supplementary Text and Figures.
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