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berkeley-express - Online in the Cloud

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This is the command berkeley-express that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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