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COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
https://combine-lab.github.io/salmon
GNU General Public License v3.0
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Bootstrapping output files #818

Closed ryanpe13002 closed 1 year ago

ryanpe13002 commented 1 year ago

To whom it may concern,

I am running Salmon with "--numBootstraps 100", but I am unsure where the bootstrapped estimates are doing. Are they incorporated directly into the *.quant.sf file, or is the only output from bootstrapping sent to the "bootstraps.gz" file? Thanks so much for any guidance you can provide!

Kindest regards, Ryan Englander

rob-p commented 1 year ago

Hi @ryanpe13002,

The bootstrap has no effect on the main quant.sf file (that is always the result of the main maximum likelihood estimate). All bootstrap samples are written to the bootstraps.gz file. If you load your data with the fishpond package in R, you can request to load the bootstraps to investigate them. Otherwise, if you use an uncertainty aware tool like swish for differential testing, it will make use of the bootstraps automatically to account for inferential uncertainty when performing differential testing.

Best, Rob