SYNOPSIS
cuffdiff [options] <transcripts.gtf> <sample1_hits.sam> <sample2_hits.sam> [... sampleN_hits.sam]
DESCRIPTION
cuffdiff v2.2.1 (Debian package) -----------------------------
- 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