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Command line summary

Table of command line options available in the two modes. options in brackets are debug options that are only available if the associated compile option has been enabled.

    count norm  
-a N y   Minimum read quality
-c <filename> y y Output counts to file rather than stdout
-d N y y Max number of reads used for normalisation
-e N   y Maximum length of transcripts used for normalisation
-f   y   Calculate and output parameter data for all models
-f     y Output full set of MCMC run data
(-g) <filename> y   Only use genes from gene list
-g N   y Limit parameter discovery to data from first N genes
-h   y y Help
-i   y   Gff identifier attribute
(-k)     y Skip Nelder Mead parameter discovery stage
-l   y   Make/read landscape file
-m union etc y   Overlap mode
-n A/B/C etc y y Normalisation mode
-o/-ou/-om <filename> y   Write reads to output file (unmatched/matched only)
-p N y y Number of threads for parameter determination
-q   y y Quiet mode
-r pos/name y   Read order
-r N   y Number of MCMC runs
-s yes/no/reverse y   Stranded
-s N   y Length of each MCMC run
-t   y   Feature type
-u <fileroot> y y Summary info sent to a set of files
(-v)   y y Initial values for discovery
(-w)   y y Output debug messages
(-x)   y y Pause before exiting program
(-y) N y y Set seed used for selecting random subset of reads
-z - y   htseq compatible