What is the expected location of bootstrap samples relative to quant.sf file ?
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fcuy047 • 0
@fcuy047-17937
Last seen 5.4 years ago

tximport states that the last known supported version of salmon is 0.6.0 but I would like to import salmon (version 0.11.3) bootstrap data using tximport (version 1.8.0)

To quote the from tximport reference manual, "If inferential replicates (Gibbs or bootstrap samples) are present in expected locations relative to the quant.sf file, tximport will import these as well"

The code snippet in tximport manual to import salmon_gibbs data from tximportData is

files <- file.path(dir, "salmon_gibbs", samples$run, "quant.sf")

But tximportData is missing the dir salmon_gibbs.

Can someone point out what is the expected location of bootstrap samples relative to quant.sf file in salmon 0.6.0 ?

TIA

PS: At the moment, the default location of bootstrap samples in relation to "sampleX/quant.sf" file is "sampleX/aux_info/bootstrap/" (generated by salmon 0.11.3). 1.8.0 version of tximport fails to read bootstrap samples

tximport tximportdata salmon • 1.0k views
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@mikelove
Last seen 4 hours ago
United States

Have you updated tximportData to the latest?

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Thank you for the solution. My tximportData package is not up to date. The latest version (1.8.0) solves the issue.

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