berkeley-express1

Streaming quantification for high-throughput sequencing

Overview

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

Releases

Unchanged in 5 releases since Debian 9 (Stretch).

9–13