xpore-dataprep1

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)