XPORE-DATAPREP(1)

NAME
xpore-dataprep - Nanopore analysis of differential RNA modifications

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

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]

  required arguments:

--eventalign EVENTALIGN
    eventalign filepath, the output from nanopolish. (default: None)

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

--out_dir OUT_DIR
    output directory. (default: None)

  optional arguments:

-h, --help
    show this help message and exit

--ensembl ENSEMBL
    ensembl version for gene-transcript mapping. (default: 91)

--species SPECIES
    species for ensembl gene-transcript mapping. (default: homo_sapiens)

--customised_genome
    if customised genome provided. (default: False)

--reference_name REFERENCE_NAME
    fasta reference name. (default: None)

--annotation_name ANNOTATION_NAME
    gtf annotation name. (default: None)

--gtf_path_or_url GTF_PATH_OR_URL
    gtf file path or url. (default: None)

--transcript_fasta_paths_or_urls TRANSCRIPT_FASTA_PATHS_OR_URLS
    transcript fasta paths or urls. (default: None)

--skip_eventalign_indexing
    skip indexing the eventalign nanopolish output. (default: False)

--genome
    to run on Genomic coordinates. Without this argument, the program will run on transcriptomic coordinates (default: False)

--n_processes N_PROCESSES
    number of processes to run. (default: 1)

--chunk_size CHUNK_SIZE
    number of lines from nanopolish eventalign.txt for processing. (default: 1000000)

--readcount_min READCOUNT_MIN
    minimum read counts per gene. (default: 1)

--readcount_max READCOUNT_MAX
    maximum read counts per gene. (default: 1000)

--resume
    with this argument, the program will resume from the previous run. (default: False)

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