HPC:cufflinks
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Cufflinks
Cufflinks version 2.2.0 is installed across all HPC nodes
Usage/default output
Cufflinks is made available via a module file:
[asrini@node061 ~]$ module load cufflinks-2.2.0 [asrini@node061 ~]$ which cufflinks /opt/software/cufflinks/2.2.0/bin/cufflinks [asrini@node061 ~]$ cufflinks cufflinks v2.2.0 linked against Boost version 104700 ----------------------------- 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 ] --seed value of random number generator seed [ default: 0 ] -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 ] --library-norm-method Method used to normalize library sizes [ 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 ] --max-mle-iterations maximum iterations allowed for MLE calculation [ default: 5000 ] --compatible-hits-norm count hits compatible with reference RNAs only [ default: FALSE ] --total-hits-norm count all hits for normalization [ default: TRUE ] --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 ] --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 ] --raw-mapped-norm Deprecated, use --library-norm-method [ DEPRECATED ] 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 ] --max-bundle-frags maximum fragments allowed in a bundle before skipping [ default: 500000 ] --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 ] --max-multiread-fraction maximum fraction of allowed multireads per transcript [ default: 0.75 ] --overlap-radius maximum gap size to fill between transfrags (in bp) [ default: 50 ] 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 Supported library normalization methods: classic-fpkm
