cuffquant(1) component of cufflinks suite


cuffdiff [,options/] ,<transcripts.gtf> <sample1_hits.sam> <sample2_hits.sam> /[... ,sampleN_hits.sam/]


cuffquant 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: ./ ]
ignore all alignment within transcripts 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 ]
Library prep used for input reads [ 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 ]
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 ]
maximum fragments allowed in a bundle before skipping [ default: 500000 ]
Maximum number of alignments allowed per fragment [ default: unlim ]
No effective length correction [ default: FALSE ]
No length correction [ default: FALSE ]

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