berkeley-express(1) 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