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CUFFDIFF

NAME

cuffdiff − component of cufflinks suite

SYNOPSIS

cuffdiff [options] <transcripts.gtf> <sample1_hits.sam> <sample2_hits.sam> [... sampleN_hits.sam]

DESCRIPTION

cuffdiff v2.2.1 () −−−−−−−−−−−−−−−−−−−−−−−−−−−−−

Supply replicate SAMs as comma separated lists for each condition: sample1_rep1.sam,sample1_rep2.sam,...sample1_repM.sam

General Options:
−o
/−−output−dir

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

−L/−−labels

comma−separated list of condition labels

−−FDR

False discovery rate used in testing [ default: 0.05 ]

−M/−−mask−file

ignore all alignment within transcripts in this file [ default: NULL ]

−C/−−contrast−file

Perform the constrasts specified in this file [ default: NULL ]

−b/−−frag−bias−correct

use bias correction − reference fasta required [ default: NULL ]

−u/−−multi−read−correct

use ’rescue method’ for multi−reads [ default: FALSE ]

−p/−−num−threads

number of threads used during quantification [ default: 1 ]

−−no−diff

Don’t generate differential analysis files [ default: FALSE ]

−−no−js−tests

Don’t perform isoform switching tests [ default: FALSE ]

−T/−−time−series

treat samples as a time−series [ default: FALSE ]

−−library−type

Library prep used for input reads [ default: below ]

−−dispersion−method

Method used to estimate dispersion models [ default: below ]

−−library−norm−method

Method used to normalize library sizes [ default: below ]

Advanced Options:
−m
/−−frag−len−mean

average fragment length (unpaired reads only) [ default: 200 ]

−s/−−frag−len−std−dev

fragment length std deviation (unpaired reads only) [ default: 80 ]

−c/−−min−alignment−count

minimum number of alignments in a locus for testing [ default: 10 ]

−−max−mle−iterations

maximum iterations allowed for MLE calculation [ default: 5000 ]

−−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 ]

−−emit−count−tables

print count tables used to fit overdispersion [ DEPRECATED ]

−−max−bundle−frags

maximum fragments allowed in a bundle before skipping [ default: 500000 ]

−−num−frag−count−draws

Number of fragment generation samples [ default: 100 ]

−−num−frag−assign−draws

Number of fragment assignment samples per generation [ default: 50 ]

−−max−frag−multihits

Maximum number of alignments allowed per fragment [ default: unlim ]

−−min−outlier−p

Min replicate p value to admit for testing [ DEPRECATED ]

−−min−reps−for−js−test

Replicates needed for relative isoform shift testing [ default: 3 ]

−−no−effective−length−correction

No effective length correction [ default: FALSE ]

−−no−length−correction

No length correction [ default: FALSE ]

−N/−−upper−quartile−norm

Deprecated, use −−library−norm−method [ DEPRECATED ]

−−geometric−norm

Deprecated, use −−library−norm−method [ DEPRECATED ]

−−raw−mapped−norm

Deprecated, use −−library−norm−method [ DEPRECATED ]

−−poisson−dispersion

Deprecated, use −−dispersion−method [ DEPRECATED ]

Debugging use only:
−−read−skip−fraction

Skip a random subset of reads this size [ default: 0.0 ]

−−no−read−pairs

Break all read pairs [ default: FALSE ]

−−trim−read−length

Trim reads to be this long (keep 5’ end) [ default: none ]

−−no−scv−correction

Disable SCV correction [ default: FALSE ]

Supported library types:

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

Supported dispersion methods:

blind per−condition poisson pooled (default)

Supported library normalization methods:

classic−fpkm geometric (default) geometric quartile

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