XPORE-DATAPREP(1) User Commands XPORE-DATAPREP(1)

xpore-dataprep - Nanopore analysis of differential RNA modifications

usage: xpore-dataprep [-h] --eventalign EVENTALIGN --summary SUMMARY --out_dir

[--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]

eventalign filepath, the output from nanopolish. (default: None)
eventalign summary filepath, the output from nanopolish. (default: None)
output directory. (default: None)

show this help message and exit
ensembl version for gene-transcript mapping. (default: 91)
species for ensembl gene-transcript mapping. (default: homo_sapiens)
if customised genome provided. (default: False)
fasta reference name. (default: None)
gtf annotation name. (default: None)
gtf file path or url. (default: None)
transcript fasta paths or urls. (default: None)
skip indexing the eventalign nanopolish output. (default: False)
to run on Genomic coordinates. Without this argument, the program will run on transcriptomic coordinates (default: False)
number of processes to run. (default: 1)
number of lines from nanopolish eventalign.txt for processing. (default: 1000000)
minimum read counts per gene. (default: 1)
maximum read counts per gene. (default: 1000)
with this argument, the program will resume from the previous run. (default: False)


This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.

May 2021 xpore-dataprep 1.0