---
name: "xpore-dataprep"
section: "1"
platform: "linux"
package: "xpore"
version: "2.1-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/xpore-dataprep"
---

# xpore-dataprep(1)

Nanopore analysis of differential RNA modifications

## 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.