Updated module order

jakobilab · Feb 23, 2018 · a0c3089 · a0c3089
1 parent e44990c
commit a0c3089
Showing 1 changed file with 69 additions and 105 deletions.
diff --git a/docs/Modules.md b/docs/Modules.md
@@ -1,21 +1,20 @@
-This project contains the framework of the circular RNA toolbox ``circtools``.
-
 # Modules
 
-Circtools currently offers four modules:
+Circtools currently offers seven modules:
 
 ```
-$ circtools
+$ circtools --help
+usage: circtools [-V] <command> [<args>]
 
             Available commands:
-
-               enrich:       circular RNA RBP enrichment scan
-               primer:       circular RNA primer design tool
+            
                detect:       circular RNA detection with DCC
                reconstruct:  circular RNA reconstruction with FUCHS
+               quickcheck:   circular RNA sequencing library quick checks
                circtest:     circular RNA statistical testing
+               enrich:       circular RNA RBP enrichment scan
                exon:         circular RNA alternative exon analysis
-               quickcheck:   circular RNA sequencing library quick checks
+               primer:       circular RNA primer design tool
 
 
 circtools: a modular, python-based framework for circRNA-related tools that
@@ -26,77 +25,18 @@ positional arguments:
 
 optional arguments:
   -h, --help     show this help message and exit
-  -V, --version  show program's version number and exit          
-               
+  -V, --version  show program's version number and exit            
 ```
 
-### detect
+## detect
 
 The ``detect`` command is an interface to [DCC](https://github.com/dieterich-lab/DCC), also developed at the Dieterich lab. Please see the corresponding [manual](https://github.com/dieterich-lab/DCC) on the GitHub project for instructions how to run DCC. The parameters supplied to circtools will be directly passed to DCC.
 
-### reconstruct
+## reconstruct
 
 The ``reconstruct`` command is an interface to [FUCHS](https://github.com/dieterich-lab/FUCHS). FUCHS is employing DCC-generated data to reconstruct circRNA structures. Please see the corresponding [manual](https://github.com/dieterich-lab/FUCHS) on the GitHub project for instructions how to run FUCHS. All parameters supplied to circtools will be directly passed to FUCHS.
 
-
-### primer
-
-The ``primer`` command is used to design and visualize primers required for follow up wet lab experiments to verify circRNA candidates. The full documentation for the ``primer`` module can be found in its own [manual](R/circtools/vignettes/plot-transcripts.md).
-
-### enrich
-
-The ``enrichment`` module may be used to identify circRNAs enriched for specific RNA binding proteins (RBP) based on DCC-identified circRNAs and processed [eCLIP](http://www.nature.com/nmeth/journal/v13/n6/full/nmeth.3810.html) data. For K526 and HepG2 cell lines plenty of this data is available through the [ENCODE](https://www.encodeproject.org/search/?type=Experiment&assay_title=eCLIP)
- project. The enrich module understands the following options:
-
-```
-usage: circtools [-h] -c CIRC_RNA_INPUT -b BED_INPUT -a ANNOTATION -g
-                 GENOME_FILE [-o OUTPUT_DIRECTORY] [-i NUM_ITERATIONS]
-                 [-p NUM_PROCESSES] [-t TMP_DIRECTORY] [-T THRESHOLD]
-                 [-P PVAL] [-H HAS_HEADER] [-F OUTPUT_FILENAME]
-                 [-I INCLUDE_FEATURES]
-
-circular RNA RBP enrichment tools
-
-optional arguments:
-  -h, --help            show this help message and exit
-
-Required options:
-  -c CIRC_RNA_INPUT, --circ-file CIRC_RNA_INPUT
-                        Path to the CircRNACount file generated by DCC
-  -b BED_INPUT, --bed-input BED_INPUT
-                        One or more BED files containing features to overlap
-  -a ANNOTATION, --annotation ANNOTATION
-                        Genome reference annotation file used to not shuffle
-                        into intragenic regions
-  -g GENOME_FILE, --genome GENOME_FILE
-                        Genome file for use with bedtools shuffle. See
-                        bedtools man page for details.
-
-Additional options:
-  -o OUTPUT_DIRECTORY, --output OUTPUT_DIRECTORY
-                        The output folder for files created by circtest
-                        [default: .]
-  -i NUM_ITERATIONS, --iterations NUM_ITERATIONS
-                        Number of iterations for CLIP shuffling [default:
-                        1000]
-  -p NUM_PROCESSES, --processes NUM_PROCESSES
-                        Number of threads to distribute the work to
-  -t TMP_DIRECTORY, --temp TMP_DIRECTORY
-                        Temporary directory used by pybedtools
-  -T THRESHOLD, --threshold THRESHOLD
-                        p-value cutoff
-  -P PVAL, --pval PVAL  p-value cutoff
-  -H HAS_HEADER, --header HAS_HEADER
-                        Defines if the circRNA input file has a header line
-                        [default: no]
-  -F OUTPUT_FILENAME, --output-filename OUTPUT_FILENAME
-                        Defines the output file prefix [default: output]
-  -I INCLUDE_FEATURES, --include-features INCLUDE_FEATURES
-                        Defines the the features which should be used for
-                        shuffling. May be specified multiple times. [default:
-                        all - shuffle over the whole genome]
-```
-### circtest
+## circtest
 
 The ``circtest`` command is an interface to [CircTest](https://github.com/dieterich-lab/CircTest). The module a a very convenient way to employ statistical testing to circRNA candidates generated with DCC without having to write an R script for each new experiment. For detailed information on the implementation itself take a look at the [CircTest documentation](https://github.com/dieterich-lab/CircTest). In essence, the module allows dynamic grouping of the columns (samples) in the DCC data. 
 
@@ -170,7 +110,62 @@ circtools circtest  -d DCC_DIR
 ```
 
 
-### exon
+## enrich
+
+The ``enrichment`` module may be used to identify circRNAs enriched for specific RNA binding proteins (RBP) based on DCC-identified circRNAs and processed [eCLIP](http://www.nature.com/nmeth/journal/v13/n6/full/nmeth.3810.html) data. For K526 and HepG2 cell lines plenty of this data is available through the [ENCODE](https://www.encodeproject.org/search/?type=Experiment&assay_title=eCLIP)
+ project. The enrich module understands the following options:
+
+```
+usage: circtools [-h] -c CIRC_RNA_INPUT -b BED_INPUT -a ANNOTATION -g
+                 GENOME_FILE [-o OUTPUT_DIRECTORY] [-i NUM_ITERATIONS]
+                 [-p NUM_PROCESSES] [-t TMP_DIRECTORY] [-T THRESHOLD]
+                 [-P PVAL] [-H HAS_HEADER] [-F OUTPUT_FILENAME]
+                 [-I INCLUDE_FEATURES]
+
+circular RNA RBP enrichment tools
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Required options:
+  -c CIRC_RNA_INPUT, --circ-file CIRC_RNA_INPUT
+                        Path to the CircRNACount file generated by DCC
+  -b BED_INPUT, --bed-input BED_INPUT
+                        One or more BED files containing features to overlap
+  -a ANNOTATION, --annotation ANNOTATION
+                        Genome reference annotation file used to not shuffle
+                        into intragenic regions
+  -g GENOME_FILE, --genome GENOME_FILE
+                        Genome file for use with bedtools shuffle. See
+                        bedtools man page for details.
+
+Additional options:
+  -o OUTPUT_DIRECTORY, --output OUTPUT_DIRECTORY
+                        The output folder for files created by circtest
+                        [default: .]
+  -i NUM_ITERATIONS, --iterations NUM_ITERATIONS
+                        Number of iterations for CLIP shuffling [default:
+                        1000]
+  -p NUM_PROCESSES, --processes NUM_PROCESSES
+                        Number of threads to distribute the work to
+  -t TMP_DIRECTORY, --temp TMP_DIRECTORY
+                        Temporary directory used by pybedtools
+  -T THRESHOLD, --threshold THRESHOLD
+                        p-value cutoff
+  -P PVAL, --pval PVAL  p-value cutoff
+  -H HAS_HEADER, --header HAS_HEADER
+                        Defines if the circRNA input file has a header line
+                        [default: no]
+  -F OUTPUT_FILENAME, --output-filename OUTPUT_FILENAME
+                        Defines the output file prefix [default: output]
+  -I INCLUDE_FEATURES, --include-features INCLUDE_FEATURES
+                        Defines the the features which should be used for
+                        shuffling. May be specified multiple times. [default:
+                        all - shuffle over the whole genome]
+```
+
+
+## exon
 
 The exon module of circtools employs the [ballgown R package](https://www.bioconductor.org/packages/release/bioc/html/ballgown.html) to combine data generated with DCC and circtest with ballgown-compatible `stringtie` output or cufflinks output converted via [tablemaker](https://github.com/leekgroup/tablemaker) in order get deeper insights into differential exon usage within circRNA candidates. 
 
@@ -230,39 +225,8 @@ Output options:
                         [Default: exon_analysis]
 ```
 
-### quickcheck
 
-The quickcheck module of circtools is an easy way to check the results of a DCC run for problems and to quickly assess the number of circRNAs in a given experiment. The module needs the mapping log files produced by STAR as well as the directory with the DCC results. The module than generates a series of figures in PDF format to assess the results.
 
-```
-usage: circtools [-h] -d DCC_DIR -s STAR_DIR -l CONDITION_LIST -g GROUPING
-                 [-o OUTPUT_DIRECTORY] [-n OUTPUT_NAME]
+## primer
 
-circular RNA sequencing library quality assessment
-
-optional arguments:
-  -h, --help            show this help message and exit
-
-Required:
-  -d DCC_DIR, --DCC DCC_DIR
-                        Path to the detect/DCC data directory
-  -s STAR_DIR, --star STAR_DIR
-                        Path to the base STAR data directory containing sub-
-                        folders with per-sample mappings
-  -l CONDITION_LIST, --condition-list CONDITION_LIST
-                        Comma-separated list of conditions which should be
-                        comparedE.g. "RNaseR +","RNaseR -"
-  -g GROUPING, --grouping GROUPING
-                        Comma-separated list describing the relation of the
-                        columns specified via -c to the sample names specified
-                        via -l; e.g. -g 1,2 and -r 3 would assign sample1 to
-                        each even column and sample 2 to each odd column
-
-Output options:
-  -o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
-                        The output directory for files created by circtest
-                        [Default: ./]
-  -n OUTPUT_NAME, --output-name OUTPUT_NAME
-                        The output name for files created by circtest
-                        [Default: quickcheck]
-```
+The ``primer`` command is used to design and visualize primers required for follow up wet lab experiments to verify circRNA candidates. The full documentation for the ``primer`` module can be found in its own [manual](R/circtools/vignettes/plot-transcripts.md).