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
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