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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
.TH XPORE-DATAPREP "1" "May 2021" "xpore-dataprep 1.0" "User Commands"
.SH NAME
xpore-dataprep \- Nanopore analysis of differential RNA modifications
.SH DESCRIPTION
usage: xpore\-dataprep [\-h] \fB\-\-eventalign\fR EVENTALIGN \fB\-\-summary\fR SUMMARY \fB\-\-out_dir\fR
.TP
OUT_DIR [\-\-ensembl ENSEMBL] [\-\-species SPECIES]
[\-\-customised_genome] [\-\-reference_name REFERENCE_NAME]
[\-\-annotation_name ANNOTATION_NAME]
[\-\-gtf_path_or_url GTF_PATH_OR_URL]
[\-\-transcript_fasta_paths_or_urls TRANSCRIPT_FASTA_PATHS_OR_URLS]
[\-\-skip_eventalign_indexing] [\-\-genome]
[\-\-n_processes N_PROCESSES] [\-\-chunk_size CHUNK_SIZE]
[\-\-readcount_min READCOUNT_MIN]
[\-\-readcount_max READCOUNT_MAX] [\-\-resume]
.SS "required arguments:"
.TP
\fB\-\-eventalign\fR EVENTALIGN
eventalign filepath, the output from nanopolish.
(default: None)
.TP
\fB\-\-summary\fR SUMMARY
eventalign summary filepath, the output from
nanopolish. (default: None)
.TP
\fB\-\-out_dir\fR OUT_DIR
output directory. (default: None)
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-ensembl\fR ENSEMBL
ensembl version for gene\-transcript mapping. (default:
91)
.TP
\fB\-\-species\fR SPECIES
species for ensembl gene\-transcript mapping. (default:
homo_sapiens)
.TP
\fB\-\-customised_genome\fR
if customised genome provided. (default: False)
.TP
\fB\-\-reference_name\fR REFERENCE_NAME
fasta reference name. (default: None)
.TP
\fB\-\-annotation_name\fR ANNOTATION_NAME
gtf annotation name. (default: None)
.TP
\fB\-\-gtf_path_or_url\fR GTF_PATH_OR_URL
gtf file path or url. (default: None)
.TP
\fB\-\-transcript_fasta_paths_or_urls\fR TRANSCRIPT_FASTA_PATHS_OR_URLS
transcript fasta paths or urls. (default: None)
.TP
\fB\-\-skip_eventalign_indexing\fR
skip indexing the eventalign nanopolish output.
(default: False)
.TP
\fB\-\-genome\fR
to run on Genomic coordinates. Without this argument,
the program will run on transcriptomic coordinates
(default: False)
.TP
\fB\-\-n_processes\fR N_PROCESSES
number of processes to run. (default: 1)
.TP
\fB\-\-chunk_size\fR CHUNK_SIZE
number of lines from nanopolish eventalign.txt for
processing. (default: 1000000)
.TP
\fB\-\-readcount_min\fR READCOUNT_MIN
minimum read counts per gene. (default: 1)
.TP
\fB\-\-readcount_max\fR READCOUNT_MAX
maximum read counts per gene. (default: 1000)
.TP
\fB\-\-resume\fR
with this argument, the program will resume from the
previous run. (default: False)
.SH AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.
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