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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:
-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 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:
-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

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

disables bias correction

disables error modelling

--aux-param-file arg
path to file containing auxiliary parameters to use instead of learning

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