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Moreover, not only do transcripts differ in their intrinsic sensitivity to NMD, the efficiency of NMD with respect to a given transcript can vary between tissues.
Although RNA-Seq has a high coverage, de novo predictions actually support more multi-exon genes than do transcripts, because of the large number of genes generated by the three de novo predictors, for example, GeneMark.hmm-ES predicted more than 40, 000 genes.
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If one must do transcript level analysis then Cufflinks and StringTie are among the best performers.
Many other papers do not perform transcript inference but still attempt to do transcript level analysis via methods which simply assign quantifications to a fixed set of annotated transcripts.
TNFα receptors, TNFRSF1B and TNFRSF1A, increased, as did transcripts that are rapidly induced by TNFα, TNFAIP3 and RIPK2 (Figure 3C).
Transcripts for Ins2 (but not Ins1) persisted in the intestines of D3+5d animals, as did transcripts for Pdx1, MafA, and Ngn3.
These 2,938 transcripts do not include transcripts that showed stable, non-changing expression levels.
What advantage do leaderless transcripts provide for survival under toxic stress?
(2) Do Cdx2 transcripts partition asymmetrically during differentiative cell-fate-directing divisions?
This group of 2430 transcripts does not include transcripts showing the most extreme differences in cross-tissue expression patterns, such as transcripts expressed exclusively on a single region.
Gretchen's suggestion made it sound so easy, as if I could just do a transcript of my performance and that would be that.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com