usage: ./MuSTA.R [-h] [-v] -i INPUT -t GTF -g GENOME [-o OUTPUT] [-p PREFIX]
[--thread THREAD] [--copy-input] [--no-lordec] [--use-lq]
[--map-qual MAP_QUAL] [--salmon-ref] [--keep]
[--sqanti-filter SQANTI_FILTER] [--sqanti-qc SQANTI_QC]
[--lordec-build-SR-graph LORDEC_BUILD_SR_GRAPH]
[--lordec-correct LORDEC_CORRECT] [--minimap2 MINIMAP2]
[--samtools SAMTOOLS] [--salmon SALMON] [--seqkit SEQKIT]
[--os {6,7}] [--force] [--verbose] [--dry-run]
MuSTA v0.0.1: Multi-Sample Transcriptome Assembly
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
INPUT:
-i INPUT, --input INPUT
An comma-separated file describing paths to input
files
-t GTF, --gtf GTF A gtf file of a reference transcriptome
-g GENOME, --genome GENOME
A fasta file of a reference genome
OUTPUT:
-o OUTPUT, --output OUTPUT
A directory where all outputs will be placed (default:
output)
-p PREFIX, --prefix PREFIX
Prefix of result files (default: musta)
CONFIGULATION:
--thread THREAD Number of threads (default: 1)
--copy-input Copy input files to a temporary directory rather than
using them as is. This option is recommended when
input files are stored in external storage systems,
and In/Out load is troublesome
--no-lordec NOT run LoRDEC in order to correct long-read sequences
with RNA-seq reads
--use-lq Activate the {long_read_lq} field of the input config
file (for using polished_lq.fastq in addition to
polished_hq.fastq)
--map-qual MAP_QUAL A threshold of mapping quality. reads with quality
larger than this threshold are selected (default: 50)
--salmon-ref Run salmon against a reference gtf as well as against
a MuSTA-derived gtf
--keep Keep intermediate files
EXTERNAL SOFTWARES:
This option group is need not to be specified unless you do not export
external softwares in the Bash environment
--sqanti-filter SQANTI_FILTER
Path to {sqanti_filter.py}
--sqanti-qc SQANTI_QC
Path to {sqanti_qc.py}
--lordec-build-SR-graph LORDEC_BUILD_SR_GRAPH
Path to {lordec-build-SR-graph}
--lordec-correct LORDEC_CORRECT
Path to {lordec-correct}
--minimap2 MINIMAP2 Path to {minimap2}
--samtools SAMTOOLS Path to {samtools}
--salmon SALMON Path to {salmon}
--seqkit SEQKIT Path to {seqkit}. This option is need not to be
specified unless you specify the {--no-lordec} option
and do not export {seqkit} in the Bash environment
MISCELLANEOUS:
--os {6,7} Redhat OS version for running qsub jobs. This option
is effective only on SHIROKANE super computer in Human
Genome Center, Japan (default: 7)
--force Re-run the entire pipeline, rather than resuming from
the suspended point of the last run.
--verbose Verbose mode
--dry-run Check the provided arguments but not run subprocesses.
All reports will be created in the current directory