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cuffdiff - component of cufflinks suite

CUFFDIFF(1) User Commands CUFFDIFF(1)

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
November 2017 cuffdiff 2.2.1+dfsg.1-2