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ploy-np committed Dec 4, 2020
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20 changes: 10 additions & 10 deletions docs/source/preparation.rst
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Expand Up @@ -9,17 +9,17 @@ Data preparation from raw reads

2. Align to transcriptome::
minimap2 -ax map-ont -uf -t 3 --secondary=no <MMI> <PATH/TO/FASTQ.GZ> > <PATH/TO/SAM> 2>> <PATH/TO/SAM_LOG>
samtools view -Sb <PATH/TO/SAM> | samtools sort -o <PATH/TO/BAM> - &>> <PATH/TO/BAM_LOG>
samtools index <PATH/TO/BAM> &>> <PATH/TO/BAM_INDEX_LOG>
minimap2 -ax map-ont -uf -t 3 --secondary=no <MMI> <PATH/TO/FASTQ.GZ> > <PATH/TO/SAM> 2>> <PATH/TO/SAM_LOG>
samtools view -Sb <PATH/TO/SAM> | samtools sort -o <PATH/TO/BAM> - &>> <PATH/TO/BAM_LOG>
samtools index <PATH/TO/BAM> &>> <PATH/TO/BAM_INDEX_LOG>

3. Resquiggle using `nanopolish eventalign <https://nanopolish.readthedocs.io/en/latest/quickstart_eventalign.html>`_::
nanopolish index -d <PATH/TO/FAST5_DIR> <PATH/TO/FASTQ_FILE>
nanopolish eventalign --reads <PATH/TO/FASTQ_FILE> \
--bam <PATH/TO/BAM_FILE> \
--genome <PATH/TO/FASTA_FILE \
--scale-events \
--summary <PATH/TO/summary.txt> \
--threads 32 > <PATH/TO/eventalign.txt>
nanopolish index -d <PATH/TO/FAST5_DIR> <PATH/TO/FASTQ_FILE>
nanopolish eventalign --reads <PATH/TO/FASTQ_FILE> \
--bam <PATH/TO/BAM_FILE> \
--genome <PATH/TO/FASTA_FILE \
--scale-events \
--summary <PATH/TO/summary.txt> \
--threads 32 > <PATH/TO/eventalign.txt>

53 changes: 31 additions & 22 deletions docs/source/scripts.rst
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Expand Up @@ -9,23 +9,24 @@ We provide 2 main scripts to run the analysis of differential RNA modifications

Input
******
Output files from `nanopolish eventalgin`. Please refer to :ref:`Data preparation <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.
--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.
==================== ========== =================== =============================================================================================================
====================== ========== =================== ============================================================================================================
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.
--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
********
Expand All @@ -45,20 +46,28 @@ File name File type Description

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.
================= ========== =============== ===============================================================================
=================== ========== =============== ==============================================================================
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 <outputtable>` for the full description.
`diffmod.log` txt Gene/Transcript ids being processed.
====================== =============== =================================================================================================================================================

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