cuffdiff(1) 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:

write all output files to this directory [ default: ./ ]
comma-separated list of condition labels
False discovery rate used in testing [ default: 0.05 ]
ignore all alignment within transcripts in this file [ default: NULL ]
Perform the constrasts specified in this file [ default: NULL ]
use bias correction - reference fasta required [ default: NULL ]
use 'rescue method' for multi-reads [ default: FALSE ]
number of threads used during quantification [ default: 1 ]
Don't generate differential analysis files [ default: FALSE ]
Don't perform isoform switching tests [ default: FALSE ]
treat samples as a time-series [ default: FALSE ]
Library prep used for input reads [ default: below ]
Method used to estimate dispersion models [ default: below ]
Method used to normalize library sizes [ default: below ]

Advanced Options:

average fragment length (unpaired reads only) [ default: 200 ]
fragment length std deviation (unpaired reads only) [ default: 80 ]
minimum number of alignments in a locus for testing [ default: 10 ]
maximum iterations allowed for MLE calculation [ default: 5000 ]
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 ]
print count tables used to fit overdispersion [ DEPRECATED ]
maximum fragments allowed in a bundle before skipping [ default: 500000 ]
Number of fragment generation samples [ default: 100 ]
Number of fragment assignment samples per generation [ default: 50 ]
Maximum number of alignments allowed per fragment [ default: unlim ]
Min replicate p value to admit for testing [ DEPRECATED ]
Replicates needed for relative isoform shift testing [ default: 3 ]
No effective length correction [ default: FALSE ]
No length correction [ default: FALSE ]
Deprecated, use --library-norm-method [ DEPRECATED ]
Deprecated, use --library-norm-method [ DEPRECATED ]
Deprecated, use --library-norm-method [ DEPRECATED ]
Deprecated, use --dispersion-method [ DEPRECATED ]

Debugging use only:

Skip a random subset of reads this size [ default: 0.0 ]
Break all read pairs [ default: FALSE ]
Trim reads to be this long (keep 5' end) [ default: none ]
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