Hi,

I am using the program Kallisto (verson 0.42.2.1) to perform pseudoalignment to a transcriptome and obtain estimated counts for each transcript. The program has an option to perform multiple bootstraps during this procedure, and I recently ran a test on one of my samples using 0, 1, 5, 10, 50, and 100 bootstraps to see at which point the estimated counts become relatively stable.

Surprisingly, the number of bootstraps did not change the estimated counts contained in the final output file abundance.tsv. However, this program also outputs an abundance file for each individual bootstrap run (compressed into abundance.h5), and the counts contained in these files were different. So, each time the program runs, the estimated counts were slightly different, but the end output file (abundance.tsv) did not change, no matter how many bootstraps were run.

If anyone could help with understanding why the estimated counts for each bootstrap would be different, but with no effect on the ultimate estimated counts, it would be appreciated!

Thanks,  
Sarah
<p>The output in the .tsv file is the maximum likelihood estimate for the expression of transcripts. That process is completely deterministic</p>

<p>The bootstrap outputs are stored in the .h5 files, they are generated by resampling the original data and finding the expression for this new dataset. This is why you will get slightly different est_counts in the bootstraps, and the amount of variation gives you an indication of how reliable the initial point estimate is.</p>
