Command line arguments

We provide 2 main scripts to run the analysis of differential RNA modifications as the following.

xpore-dataprep

  • Input

Output files from nanopolish eventalgin. Please refer to Data preparation for the full Nanopolish command.

Argument name

Required

Default value

Description

–eventalign=FILE

Yes

NA

Eventalign filepath, the output from nanopolish.

–out_dir=DIR

Yes

NA

Output directory.

–gtf_path_or_url

No

NA

GTF file path or url used for mapping transcriptomic to genomic coordinates.

–transcript_fasta_paths_or_urls

No

NA

Transcript FASTA paths or urls used for mapping transcriptomic to genomic coordinates.

–skip_eventalign_indexing

No

False

To skip indexing the eventalign nanopolish output.

–genome

No

False

To run on Genomic coordinates. Without this argument, the program will run on transcriptomic coordinates.

–n_processes=NUM

No

1

Number of processes to run.

–readcount_max=NUM

No

1000

Maximum read counts per gene.

–readcount_min=NUM

No

1

Minimum read counts per gene.

–resume

No

False

With this argument, the program will resume from the previous run.

  • Output

File name

File type

Description

eventalign.index

csv

File index indicating the position in the eventalign.txt file (the output of nanopolish eventalign) where the segmentation information of each read index is stored, allowing a random access.

data.json

json

Intensity level mean for each position.

data.index

csv

File index indicating the position in the data.json file where the intensity level means across positions of each gene is stored, allowing a random access.

data.log

txt

Gene ids being processed.

data.readcount

csv

Summary of readcounts per gene.

xpore-diffmod

  • Input

Output files from xpore-dataprep.

Argument name

Required

Default value

Description

–config=FILE

Yes

NA

YAML configurtaion filepath.

–n_processes=NUM

No

1

Number of processes to run.

–save_models

No

False

With this argument, the program will save the model parameters for each id.

–resume

No

False

With this argument, the program will resume from the previous run.

–ids=LIST

No

[]

Gene / Transcript ids to model.

  • Output

File name

File type

Description

diffmod.table

csv

Output table information of differential modification rates. Please refer to Output table description for the full description.

diffmod.log

txt

Gene/Transcript ids being processed.

xpore-postprocessing

  • Input

The diffmod.table file from xpore-diffmod.

Argument name

Required

Description

–diffmod_dir

Yes

Path of the directory containing diffmod.table.