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
-
-
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.
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM
Comment