updated doc

docs/source/index.rst

@@ -24,6 +24,8 @@ Contents
    installation
    quickstart
    configuration
+   preparation
+   scripts
    api
 
 Contacts

docs/source/preparation.rst

@@ -0,0 +1,23 @@
+.. _preparation:
+
+Data preparation from raw reads
+===================================
+
+1. After obtaining fast5 files, the first step is to basecall them. Below is an example script to run Guppy basecaller. You can find more detail about basecalling at `Oxford nanopore Technologies <https://nanoporetech.com>`_::
+
+    guppy_basecaller -i </PATH/TO/FAST5> -s </PATH/TO/FASTQ> --flowcell <FLOWCELL_ID> --kit <KIT_ID> --device auto -q 0 -r   
+
+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>
+
+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>
+

docs/source/scripts.rst

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+.. _scripts:
+
+Scripts
+==========
+
+We provide 2 main scripts to run the analysis of differential RNA modifications as the following.
+
+1. ``xpore-dataprep``
+
+=================  ==========  =============== =============
+Argument name(s)    Required    Default value   Description
+=================  ==========  =============== =============
+--eventalign        Yes             NA          eventalign filepath, the output from nanopolish.         
+--summary           Yes             NA          eventalign summary filepath, the output from nanopolish.
+--out_dir           Yes             NA          output directory.
+=================  ==========  =============== =============
+
+
+2. ``xpore-diffmod``
+