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.