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pachterlab / kallisto

Near-optimal RNA-Seq quantification
https://pachterlab.github.io/kallisto
BSD 2-Clause "Simplified" License
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QA: Where can I find bootstrap summary statistics? #142

Closed holgerbrandl closed 6 years ago

holgerbrandl commented 7 years ago

I managed to run kallisto with bootstrapping. Now I'm struggling to get some summary statistics. I can read the raw bootstrap results (e.g. in R) with

require(rhdf5)
bs_data = h5read(files[1],"bootstrap/bs0")

I've tried tximport package already but could not find a corresponding method.

However, I'd be rather curious to get gene-level summary estimates about the uncertainty of expression estimates. Is this part of the hdf5 or do I need to calculate those numbers myself? If the latter applies, are there some public code-bits I could reuse?

holgerbrandl commented 6 years ago

I'd be still curious to learn more about bootstrapping support in kallisto, so feel welcome if you need more info to process my request.

pmelsted commented 6 years ago

Gene level estimates are not stored in the hdf5 files, but are computed with sleuth, https://github.com/pachterlab/sleuth

The user group, https://groups.google.com/forum/#!forum/kallisto-sleuth-users is a better place to get help on using the sleuth functions. Also take a look at http://pachterlab.github.io/sleuth/ and the sleuth walk-throughs to see how sleuth is used.

holgerbrandl commented 6 years ago

Ok, thanks. Actually I was briefly looking into the sleuth-repo already but its REAMDE stated that

It makes use of quantification uncertainty estimates obtained via kallisto for accurate differential analysis of isoforms

That's why I ended up here.

mschilli87 commented 6 years ago

@holgerbrandl: Both can be correct as you asked for gene level estimates. IRC, kallisto estimates transcript (isoform) level uncertanties, which are read by sleuth and summarized to the gene-level.

holgerbrandl commented 6 years ago

My bad, I actually wanted to to access the "transcript level uncertainties". Where are they stored? I somehow can not find them when reading in h5 or tsv output from kallisto.

pmelsted commented 6 years ago

The h5 files contain the complete quantifications of each bootstrap. If you want summaries I recommend using sleuth to compute them, take a look at get_bootstrap_summary in sleuth, which should give you what you need.

holgerbrandl commented 6 years ago

Cool, thanks (also for your patience), that's the answer I was looking for.