berkeley-express(1)

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