Man page - cuffnorm(1)
Manual
| CUFFNORM(1) | User Commands | CUFFNORM(1) |
NAME
cuffnorm - component of cufflinks suite
SYNOPSIS
cuffnorm [options] <transcripts.gtf> <sample1_expr.cxb> <sample2_expr.cxb> [... sampleN_expr.cxb]
DESCRIPTION
cuffnorm v2.2.1 (Debian package) -----------------------------
- Supply replicate CXB files as comma separated lists for each condition: sample1_rep1.cxb,sample1_rep2.cxb,...sample1_repM.cxb
General Options:
- -o/--output-dir
- write all output files to this directory [ default: ./ ]
- -L/--labels
- comma-separated list of condition labels
- --norm-standards-file
- Housekeeping/spike genes to normalize libraries [ default: NULL ]
- -p/--num-threads
- number of threads used during quantification [ default: 1 ]
- --library-type
- Library prep used for input reads [ default: below ]
- --library-norm-method
- Method used to normalize library sizes [ default: below ]
- --output-format
- Format for output tables [ default: below ]
Advanced Options:
- --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 ]
Supported library types:
- ff-firststrand ff-secondstrand ff-unstranded fr-firststrand fr-secondstrand fr-unstranded (default) transfrags
Supported library normalization methods:
- classic-fpkm geometric (default) geometric quartile
Supported output formats:
- cuffdiff simple-table (default)
| August 2024 | cuffnorm 2.2.1+dfsg.1-10 |