[MODIF] doc update

Author: nservant

config-hicpro.txt

@@ -14,7 +14,7 @@ RAW_DIR = rawdata
 ## SYSTEM AND SCHEDULER - Start Editing Here !!
 #######################################################################
 N_CPU = 2
-SORT_RAM = 768M
+SORT_RAM = 1000M
 LOGFILE = hicpro.log
 
 JOB_NAME = 

doc/MANUAL.md

@@ -45,14 +45,15 @@ In order to process the raw data, HiC-Pro requires three annotation files. Note
 
 Copy and edit the configuration file *'config-hicpro.txt'* in your local folder. The '[]' options are optional and can be undefined.
 
-| SYSTEM         |                                        |
-|----------------|----------------------------------------|
-| N_CPU          | Number of CPU allows per job           |
-| LOGFILE        | Name of the main log file              |
-| [JOB_NAME  ]   | Name of the job on the custer          |
-| [JOB_MEM]      | Memory (RAM) required per job          |
-| [JOB_WALLTIME] | WallTime allows per job                |
-| [JOB_MAIL]     | User mail for PBS/Torque report        |
+| SYSTEM         |                                                                                                                      |
+|----------------|----------------------------------------------------------------------------------------------------------------------|
+| N_CPU          | Number of CPU allows per job                                                                                         |
+| SORT_RAM       | The memory for samtools sort (in Mo). Note that this number will be divided by the N_CPU to have a memory per thread |
+| LOGFILE        | Name of the main log file                                                                                            |
+| [JOB_NAME  ]   | Name of the job on the custer                                                                                        |
+| [JOB_MEM]      | Memory (RAM) required per job                                                                                        |
+| [JOB_WALLTIME] | WallTime allows per job                                                                                              |
+| [JOB_MAIL]     | User mail for PBS/Torque report                                                                                      |
 
 ----------------
 

doc/UTILS.md

@@ -52,12 +52,12 @@ Finally, note that multiple restriction enzymes can also be provided (space sepa
 ### make_viewpoints.py OR 'How can I generate a BED profile from a given viewpoints ?'
 
 The make_viewpoints.py script was initially designed in the context of capture-C data.  
-For a given anchor (i.e. capture site), it allows to generate a track file with all interacting fragments.  
+For a list of anchors (i.e. capture sites), it allows to generate track files with all interacting fragments.  
 Regions around the capture are usually excluded from the profile ('-e' parameter)
 
 ```
    ## Generate a viewpoints from capture site
-   HICPRO_PATH/bin/utils/make_viewpoints -i hicpro_res/hic_results/data/dixon_2M/dixon_2M_allValidPairs  -f HICPRO_PATH/data_info/HindIII_resfrag_hg19.bed -t mycapture.bed -e 1000 -v > capture.bedgraph
+   HICPRO_PATH/bin/utils/make_viewpoints -i hicpro_res/hic_results/data/dixon_2M/dixon_2M_allValidPairs -f HICPRO_PATH/data_info/HindIII_resfrag_hg19.bed -t mycapture.bed -e 1000 -o OUTPUT_DIR/output_ -v
 ```
 
 ### hicpro2juicebox.sh OR 'How can I load my HiC-Pro data into Juicebox visualization software ?'
@@ -68,10 +68,10 @@ This utility requires HiC-Pro version 2.7.6 or later, and the installation of [J
 
 ```
    ## Convert HiC-Pro output to Juicebox input
-   HICPRO_PATH/bin/utils/hicpro2juicebox.sh -i hicpro_res/hic_results/data/dixon_2M/dixon_2M_allValidPairs -g chrom_hg19.sizes -j /usr/local/juicebox/juicebox_clt_1.4.jar
+   HICPRO_PATH/bin/utils/hicpro2juicebox.sh -i hicpro_res/hic_results/data/dixon_2M/dixon_2M_allValidPairs -g chrom_hg19.sizes -j /usr/local/juicer/juicer_tools.1.7.5_linux_x64_jcuda.0.8.jar
 
    ## Convert HiC-Pro output to Juicebox input up to restriction fragment resolution
-   HICPRO_PATH/bin/utils/hicpro2juicebox.sh -i hicpro_res/hic_results/data/dixon_2M/dixon_2M_allValidPairs -g chrom_hg19.sizes -j /usr/local/juicebox/juicebox_clt_1.4.jar -f  HICPRO_PATH/data_info/HindIII_resfrag_hg19.bed
+   HICPRO_PATH/bin/utils/hicpro2juicebox.sh -i hicpro_res/hic_results/data/dixon_2M/dixon_2M_allValidPairs -g chrom_hg19.sizes -j /usr/local/juicer/juicer_tools.1.7.5_linux_x64_jcuda.0.8.jar -f  HICPRO_PATH/data_info/HindIII_resfrag_hg19.bed
 ```
 
 ### sparseToDense.py OR 'How can I convert HiC-Pro output into dense format ?'
@@ -112,6 +112,8 @@ See https://github.com/mirnylab/cooler for .cool Hi-C data format. The path to c
    HICPRO_PATH/bin/utils/hicpro2higlass.sh -i hic_results/data/dixon_2M/dixon_2M_allValidPairs -r 40000 -c chrom_hg19.sizes -n
 ```
 
+Note that you should use the `--float` option for iced normalized data.
+
 ### split_sparse.py OR 'How can I split my HiC-Pro sparse format ?'
 
 This utility allows to split a genome-wide contact maps generated by HiC-Pro into per-chromosome interaction maps.