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.. _cmd:
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 :ref:`Data preparation <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 :ref:`Output table description <outputtable>` 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``.
====================== =============== =======================================================================
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