Utility of Kallisto bootstraps when not using sleuth downstream

Question

[kautilya]

Does the bootstrap option for kallisto have any utility if sleuth is not going to be used downstream? In a small test I did the abundance.tsv output files are identical with/without the option being used.

[James Ashmore]

Bootstrapping provides a measure of the accuracy of the estimated abundances. The abundance values are consistent regardless of the number of bootstraps. See the answers here. Conventional packages such as DESeq2 or edgeR do not readily accommodate this extra information so you may as well run Kallisto with no bootstrapping.

Answer 1

[Kevin Blighe]

The bootstrapped estimates are stored in the HDF5 file (extension h5). The regular abundance.tsv file will always contain the same values because no bootstrapped values are ever stored in it.

So, you can access and use the bootstrapped values by accessing the HDF5 file. You can do this with:

kallisto h5dump abundances.h5

Kevin