---
name: "berkeley-express"
section: "1"
platform: "linux"
package: "berkeley-express"
version: "1.5.3+dfsg-3+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/berkeley-express"
---

# berkeley-express(1)

Streaming quantification for high-throughput sequencing

## 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