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cuffnorm - component of cufflinks suite

CUFFNORM(1) User Commands CUFFNORM(1)

NAME

cuffnorm - component of cufflinks suite

SYNOPSIS

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

DESCRIPTION

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:

-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)
November 2017 cuffnorm 2.2.1+dfsg.1-2