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HMM code and input files
Contains data and code to run an HMM optimisation for Hermes insertion data.
Contains:
The predictors of insertion density:
predictors.2016-10-06.tar.gz
includes:
insertion motif similarity score (IMSS)
nucleosome density scores
hidden Markov Model R code
transposon-hmm-7-cross-validation.R
sample config file
log.III.5A.tr-even.config.r
#the code is run like so:
cat transposon-hmm-7-cross-validation.R | \
R --slave --args config.r input.Rda
We also include:
sample input files:
all-log.and-predictors.2016-10-06.txt.Rda
Sample output files:
log.all-model5A.hmmresult.table.Rda
Hermes-containing read mapping scores:
mapping.scores.txt.gz
