SYNOPSIS

DESCRIPTION

Supply replicate CXB files as comma separated lists for each condition: sample1_rep1.cxb,sample1_rep2.cxb,...sample1_repM.cxb

General Options:

-o/--output-dir

write all output files to this directory [ default: ./ ]

-L/--labels

comma-separated list of condition labels

--norm-standards-file

Housekeeping/spike genes to normalize libraries [ default: NULL ]

-p/--num-threads

number of threads used during quantification [ default: 1 ]

--library-type

Library prep used for input reads [ default: below ]

--library-norm-method

Method used to normalize library sizes [ default: below ]

--output-format

Format for output tables [ default: below ]

Advanced Options:

--compatible-hits-norm

count hits compatible with reference RNAs only [ default: TRUE ]

--total-hits-norm

count all hits for normalization [ default: FALSE ]

-v/--verbose

log-friendly verbose processing (no progress bar) [ default: FALSE ]

-q/--quiet

log-friendly quiet processing (no progress bar) [ default: FALSE ]

--seed

value of random number generator seed [ default: 0 ]

--no-update-check

do not contact server to check for update availability[ default: FALSE ]

Supported library types:

ff-firststrand ff-secondstrand ff-unstranded fr-firststrand fr-secondstrand fr-unstranded (default) transfrags

Supported library normalization methods:

classic-fpkm geometric (default) geometric quartile

Supported output formats:

cuffdiff simple-table (default)