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. |