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EXPRESS(1) User Commands EXPRESS(1)


berkeley-express - Streaming quantification for high-throughput sequencing


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 sequence file in fasta format
read alignment file in SAM or BAM format

Standard Options:

produce help message
write all output files to this directory
run preprocess script for eXpressD
prior estimate for average fragment length
prior estimate for fragment length std deviation
path to a file containing haplotype pairs
number of additional batch EM rounds after initial online round
after initial online round
maximum allowed length of a read
output alignments (sam/bam) with probabilistic assignments
output alignments (sam/bam) with sampled assignments
accept only forward->reverse alignments (second-stranded protocols)
accept only reverse->forward alignments (first-stranded protocols)
accept only forward single-end alignments (second-stranded protocols)
accept only reverse single-end alignments (first-stranded protocols)
disables automatic check for update via web
prints all logging messages to stderr

Advanced Options:

sets the 'forgetting factor' parameter (0.5 < c <= 1)
specifies library size for FPKM instead of calculating from alignments
sets the maximum allowed indel size, affecting geometric indel prior
calculate and output covariance matrix
sets the strength of the prior, per bp
sets the number of fragments to process, disabled with 0
sets number of fragments after which to stop updating auxiliary parameters
disables bias correction
disables error modelling
path to file containing auxiliary parameters to use instead of learning

February 2015 express 1.5.1