Cufflinks significance testing

[Astro22]

Good day all,

I am new to analyzing RNA-seq data and am trying to understand how cufflinks calls a transcript significant or not between two conditions?

I ask this because when I assess some of the transcripts that are called not significant by cufflinks with an ANOVA or Kruskal-Wallis test, I get that it is significantly different...

What should I do in a scenario like that? Should I go with cufflinks or other statistical tests?

I would appreciate any assistance in this matter..

Thank you

[pbluescript]

You should go with a method designed to correct for multiple testing. Something like Cufflinks, DESeq, rsem, etc. will probably do a better job than a single test.