cuffdiff − component of cufflinks suite
cuffdiff [options] <transcripts.gtf> <sample1_hits.sam> <sample2_hits.sam> [... sampleN_hits.sam]
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