table of contents
| EXPRESS(1) | User Commands | EXPRESS(1) |
NAME¶
berkeley-express - Streaming quantification for high-throughput sequencing
DESCRIPTION¶
File Usage: express [options] <target_seqs.fa> <hits.(sam/bam)> Piped Usage: bowtie [options] -S <index> <reads.fq> | express [options] <target_seqs.fa>
Required arguments:¶
- <target_seqs.fa>
- target sequence file in fasta format
- <hits.(sam/bam)>
- read alignment file in SAM or BAM format
Standard Options:¶
- -h [ --help ]
- produce help message
- -o [ --output-dir ] arg (=.)
- write all output files to this directory
- -D [ --preprocess ]
- run preprocess script for eXpressD
- -m [ --frag-len-mean ] arg (=200)
- prior estimate for average fragment length
- -s [ --frag-len-stddev ] arg (=80)
- prior estimate for fragment length std deviation
- -H [ --haplotype-file ] arg
- path to a file containing haplotype pairs
- -B [ --additional-batch ] arg (=0)
- number of additional batch EM rounds after initial online round
- -O [ --additional-online ] arg (=0) number of additional online EM rounds
- after initial online round
- -L [ --max-read-len ] arg (=250)
- maximum allowed length of a read
- --output-align-prob
- output alignments (sam/bam) with probabilistic assignments
- --output-align-samp
- output alignments (sam/bam) with sampled assignments
- --fr-stranded
- accept only forward->reverse alignments (second-stranded protocols)
- --rf-stranded
- accept only reverse->forward alignments (first-stranded protocols)
- --f-stranded
- accept only forward single-end alignments (second-stranded protocols)
- --r-stranded
- accept only reverse single-end alignments (first-stranded protocols)
- --no-update-check
- disables automatic check for update via web
- --logtostderr
- prints all logging messages to stderr
Advanced Options:¶
- -f [ --forget-param ] arg (=0.84999999999999998)
- sets the 'forgetting factor' parameter (0.5 < c <= 1)
- --library-size arg
- specifies library size for FPKM instead of calculating from alignments
- --max-indel-size arg (=10)
- sets the maximum allowed indel size, affecting geometric indel prior
- --calc-covar
- calculate and output covariance matrix
- --expr-alpha arg (=0.0050000000000000001)
- sets the strength of the prior, per bp
- --stop-at arg (=0)
- sets the number of fragments to process, disabled with 0
- --burn-out arg (=5000000)
- sets number of fragments after which to stop updating auxiliary parameters
- --no-bias-correct
- disables bias correction
- --no-error-model
- disables error modelling
- --aux-param-file arg
- path to file containing auxiliary parameters to use instead of learning
| February 2015 | express 1.5.1 |