Provided by: cufflinks_2.1.1-4_amd64 
NAME
cufflinks - Transcript assembly, differential expression, and differential regulation for
RNA-Seq
DESCRIPTION
see online page http://cufflinks.cbcb.umd.edu/manual.html
SYNOPSIS
cufflinks [options] <hits.sam>
OPTIONS
-o/--output-dir
write all output files to this directory [ default: ./ ]
-p/--num-threads
number of threads used during analysis [ default: 1 ]
-G/--GTF
quantitate against reference transcript annotations
-g/--GTF-guide
use reference transcript annotation to guide assembly
-M/--mask-file
ignore all alignment within transcripts in this file
-b/--frag-bias-correct
use bias correction - reference fasta required [ default: NULL ]
-u/--multi-read-correct
use 'rescue method' for multi-reads (more accurate) [ default: FALSE ]
--library-type
library prep used for input reads [ default: below ]
Advanced Abundance Estimation 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 ]
--upper-quartile-norm
use upper-quartile normalization [ default: FALSE ]
--max-mle-iterations
maximum iterations allowed for MLE calculation [ default: 5000 ]
--num-importance-samples
number of importance samples for MAP restimation [ default: 1000 ]
--compatible-hits-norm
count hits compatible with reference RNAs only [ default: FALSE ]
--total-hits-norm
count all hits for normalization [ default: TRUE ]
Advanced Assembly Options:
-L/--label
assembled transcripts have this ID prefix [ default: CUFF ]
-F/--min-isoform-fraction
suppress transcripts below this abundance level [ default: 0.10 ]
-j/--pre-mrna-fraction
suppress intra-intronic transcripts below this level [ default: 0.15 ]
-I/--max-intron-length
ignore alignments with gaps longer than this [ default: 300000 ]
-a/--junc-alpha
alpha for junction binomial test filter [ default: 0.001 ]
-A/--small-anchor-fraction
percent read overhang taken as 'suspiciously small' [ default: 0.09 ]
--min-frags-per-transfrag
minimum number of fragments needed for new transfrags [ default: 10 ]
--overhang-tolerance
number of terminal exon bp to tolerate in introns [ default: 8 ]
--max-bundle-length
maximum genomic length allowed for a given bundle [ default:3500000 ]
--min-intron-length
minimum intron size allowed in genome [ default: 50 ]
--trim-3-avgcov-thresh
minimum avg coverage required to attempt 3' trimming [ default: 10 ]
--trim-3-dropoff-frac
fraction of avg coverage below which to trim 3' end [ default: 0.1 ]
Advanced Reference Annotation Guided Assembly Options:
--no-faux-reads
disable tiling by faux reads [ default: FALSE ]
--3-overhang-tolerance
overhang allowed on 3' end when merging with reference[ default: 600 ]
--intron-overhang-tolerance
overhang allowed inside reference intron when merging [ default: 30 ]
Advanced Program Behavior Options:
-v/--verbose
log-friendly verbose processing (no progress bar) [ default: FALSE ]
-q/--quiet
log-friendly quiet processing (no progress bar) [ default: FALSE ]
--no-update-check
do not contact server to check for update availability[ default: FALSE ]
Supported library types:
ff-firststrand ff-secondstrand ff-unstranded fr-firststrand fr-secondstrand
fr-unstranded (default) transfrags
cufflinks v1.0.2 linked against Boost version 104601 ----------------------------- Usage:
cufflinks [options] <hits.sam> General Options:
-o/--output-dir
write all output files to this directory [ default: ./ ]
-p/--num-threads
number of threads used during analysis [ default: 1 ]
-G/--GTF
quantitate against reference transcript annotations
-g/--GTF-guide
use reference transcript annotation to guide assembly
-M/--mask-file
ignore all alignment within transcripts in this file
-b/--frag-bias-correct
use bias correction - reference fasta required [ default: NULL ]
-u/--multi-read-correct
use 'rescue method' for multi-reads (more accurate) [ default: FALSE ]
--library-type
library prep used for input reads [ default: below ]
Advanced Abundance Estimation 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 ]
--upper-quartile-norm
use upper-quartile normalization [ default: FALSE ]
--max-mle-iterations
maximum iterations allowed for MLE calculation [ default: 5000 ]
--num-importance-samples
number of importance samples for MAP restimation [ default: 1000 ]
--compatible-hits-norm
count hits compatible with reference RNAs only [ default: FALSE ]
--total-hits-norm
count all hits for normalization [ default: TRUE ]
Advanced Assembly Options:
-L/--label
assembled transcripts have this ID prefix [ default: CUFF ]
-F/--min-isoform-fraction
suppress transcripts below this abundance level [ default: 0.10 ]
-j/--pre-mrna-fraction
suppress intra-intronic transcripts below this level [ default: 0.15 ]
-I/--max-intron-length
ignore alignments with gaps longer than this [ default: 300000 ]
-a/--junc-alpha
alpha for junction binomial test filter [ default: 0.001 ]
-A/--small-anchor-fraction
percent read overhang taken as 'suspiciously small' [ default: 0.09 ]
--min-frags-per-transfrag
minimum number of fragments needed for new transfrags [ default: 10 ]
--overhang-tolerance
number of terminal exon bp to tolerate in introns [ default: 8 ]
--max-bundle-length
maximum genomic length allowed for a given bundle [ default:3500000 ]
--min-intron-length
minimum intron size allowed in genome [ default: 50 ]
--trim-3-avgcov-thresh
minimum avg coverage required to attempt 3' trimming [ default: 10 ]
--trim-3-dropoff-frac
fraction of avg coverage below which to trim 3' end [ default: 0.1 ]
Advanced Reference Annotation Guided Assembly Options:
--no-faux-reads
disable tiling by faux reads [ default: FALSE ]
--3-overhang-tolerance
overhang allowed on 3' end when merging with reference[ default: 600 ]
--intron-overhang-tolerance
overhang allowed inside reference intron when merging [ default: 30 ]
Advanced Program Behavior Options:
-v/--verbose
log-friendly verbose processing (no progress bar) [ default: FALSE ]
-q/--quiet
log-friendly quiet processing (no progress bar) [ default: FALSE ]
--no-update-check
do not contact server to check for update availability[ default: FALSE ]
Supported library types:
ff-firststrand ff-secondstrand ff-unstranded fr-firststrand fr-secondstrand
fr-unstranded (default) transfrags