NAME

cuffnorm - component of cufflinks suite

SYNOPSIS

cuffnorm [options] <transcripts.gtf> <sample1_expr.cxb> <sample2_expr.cxb> [... sampleN_expr.cxb]

cuffnorm v2.2.1 (Debian package) -----------------------------

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

-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 ]

--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 ]

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