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Question: What is the expected location of bootstrap samples relative to quant.sf file ?
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gravatar for fcuy047
22 days ago by
fcuy0470
fcuy0470 wrote:

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

ADD COMMENTlink modified 22 days ago • written 22 days ago by fcuy0470
1
gravatar for Michael Love
22 days ago by
Michael Love20k
United States
Michael Love20k wrote:

Have you updated tximportData to the latest?

ADD COMMENTlink written 22 days ago by Michael Love20k

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

ADD REPLYlink modified 22 days ago • written 22 days ago by fcuy0470
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