Man page - cufflinks(1)

Manual

CUFFLINKS(1) User Commands CUFFLINKS(1)

cufflinks - component of cufflinks suite

cufflinks [options] <hits.sam>

cufflinks v2.2.1 linked against Boost version 108300 -----------------------------

write all output files to this directory [ default: ./ ]
number of threads used during analysis [ default: 1 ]
value of random number generator seed [ default: 0 ]
quantitate against reference transcript annotations
use reference transcript annotation to guide assembly
ignore all alignment within transcripts in this file
use bias correction - reference fasta required [ default: NULL ]
use 'rescue method' for multi-reads (more accurate) [ default: FALSE ]
library prep used for input reads [ default: below ]
Method used to normalize library sizes [ default: below ]

average fragment length (unpaired reads only) [ default: 200 ]
fragment length std deviation (unpaired reads only) [ default: 80 ]
maximum iterations allowed for MLE calculation [ default: 5000 ]
count hits compatible with reference RNAs only [ default: FALSE ]
count all hits for normalization [ default: TRUE ]
Number of fragment generation samples [ default: 100 ]
Number of fragment assignment samples per generation [ default: 50 ]
Maximum number of alignments allowed per fragment [ default: unlim ]
No effective length correction [ default: FALSE ]
No length correction [ default: FALSE ]
Deprecated, use --library-norm-method [ DEPRECATED ]
Deprecated, use --library-norm-method [ DEPRECATED ]

assembled transcripts have this ID prefix [ default: CUFF ]
suppress transcripts below this abundance level [ default: 0.10 ]
suppress intra-intronic transcripts below this level [ default: 0.15 ]
ignore alignments with gaps longer than this [ default: 300000 ]
alpha for junction binomial test filter [ default: 0.001 ]
percent read overhang taken as 'suspiciously small' [ default: 0.09 ]
minimum number of fragments needed for new transfrags [ default: 10 ]
number of terminal exon bp to tolerate in introns [ default: 8 ]
maximum genomic length allowed for a given bundle [ default:3500000 ]
maximum fragments allowed in a bundle before skipping [ default: 500000 ]
minimum intron size allowed in genome [ default: 50 ]
minimum avg coverage required to attempt 3' trimming [ default: 10 ]
fraction of avg coverage below which to trim 3' end [ default: 0.1 ]
maximum fraction of allowed multireads per transcript [ default: 0.75 ]
maximum gap size to fill between transfrags (in bp) [ default: 50 ]

disable tiling by faux reads [ default: FALSE ]
--3-overhang-tolerance
overhang allowed on 3' end when merging with reference[ default: 600 ]
overhang allowed inside reference intron when merging [ default: 30 ]

log-friendly verbose processing (no progress bar) [ default: FALSE ]
log-friendly quiet processing (no progress bar) [ default: FALSE ]
do not contact server to check for update availability[ default: FALSE ]

ff-firststrand ff-secondstrand ff-unstranded fr-firststrand fr-secondstrand fr-unstranded (default) transfrags

classic-fpkm
August 2024 cufflinks 2.2.1+dfsg.1-10