SYNOPSIS

DESCRIPTION

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