cuffnorm(1) component of cufflinks suite


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


cuffnorm v2.2.1 () -----------------------------
Supply replicate CXB files as comma separated lists for each condition: sample1_rep1.cxb,sample1_rep2.cxb,...sample1_repM.cxb

General Options:

write all output files to this directory [ default: ./ ]
comma-separated list of condition labels
Housekeeping/spike genes to normalize libraries [ default: NULL ]
number of threads used during quantification [ default: 1 ]
Library prep used for input reads [ default: below ]
Method used to normalize library sizes [ default: below ]
Format for output tables [ default: below ]

Advanced Options:

count hits compatible with reference RNAs only [ default: TRUE ]
count all hits for normalization [ default: FALSE ]
log-friendly verbose processing (no progress bar) [ default: FALSE ]
log-friendly quiet processing (no progress bar) [ default: FALSE ]
value of random number generator seed [ default: 0 ]
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)