Scripts

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.

• Usage example

Argument name(s)	Required	Default value	Description
–eventalign=FILE	Yes	NA	Eventalign filepath, the output from nanopolish.
–summary=FILE	Yes	NA	Eventalign summary filepath, the output from nanopolish.
–out_dir=DIR	Yes	NA	Output directory.
–ensembl=NUM	No	91	Ensembl version for gene-transcript mapping.
–species=STR	No	homo_sapiens	Species for ensembl gene-transcript mapping.
–customised_genome	No	False	If customised genome provided.
–reference_name	No	NA	fasta reference name.
–annotation_name	No	NA	gtf annotation name.
–gtf_path_or_url	No	NA	gtf file path or url.
–transcript_fasta_paths_or_urls	No	NA	Transcript fasta paths or urls.
–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.
–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.

• Usage example

Argument name(s)	Required	Default value	Description
–config=FILE	Yes	NA	Yaml configuraion 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.