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 |