Sleuth Table - identical q-values

Question

[arussell3483]

Hello,

I have finished running kallisto and am working on running sleuth with my dataset. I have completed the initial walkthrough (as can be seen here: https://pachterlab.github.io/sleuth_walkthroughs/trapnell/analysis.html) successfully. My own dataset is very similar to this sample set, with 12 samples and 2 conditions. I can run through sleuth with my dataset, but the output is not what I expected. I have 21,985 transcripts, but the q-values are repeating. For example, very large groups (100+) of transcripts will all have the same q-value. As far as I can tell, this is occurring throughout all 21,985 transcripts. Has anyone else run into this problem?

Thank you!