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