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 ?
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