Merge branch 'master' of https://github.com/nservant/HiC-Pro

Author: nservant

README.rst

@@ -58,7 +58,7 @@ Bowtie >2.2.2 is strongly recommanded for allele specific analysis.
 +---------------+-----------------------------------------------------------------------------+
 | SYSTEM CONFIGURATION                                                                        |
 +===============+=============================================================================+
-| PREFIX        | Path to installation folder                                                           |
+| PREFIX        | Path to installation folder                                                 |
 +---------------+-----------------------------------------------------------------------------+
 | BOWTIE2_PATH  | Full path the bowtie2 installation directory                                |
 +---------------+-----------------------------------------------------------------------------+

doc/MANUAL.rst

@@ -238,13 +238,22 @@ See the :ref:`results <RES>` section for more information.
 
 * *bowtie_results*
 
-The *bowtie_results* folder contains the results of the reads mapping. The results of first mapping step are available in the *bwt2_glob* folder, and the seconnd step in the *bwt2_loc* folder. Final BAM files, reads pairing, and mapping statistics are available on the *bwt2* folder.
+The *bowtie_results* folder contains the results of the reads mapping. The results of first mapping step are available in the *bwt2_glob* folder, and the seconnd step in the *bwt2_loc* folder. Final BAM files, reads pairing, and mapping statistics are available on the *bwt2* folder. Note that once HiC-Pro has been run, all files in *bwt2_glob* or *bwt2_loc* folders can be removed. These files take a significant amount of disk space and are not useful anymore.
 
 * *hic_results*
 
 | This folder contains all Hi-C processed data, and is further divided in several sub-folders.
 | The *data* folder is used to store the valid interaction products (*.validPairs*), as well as other statisics files.
+
+| The *validPairs* are stored using a simple tab-delimited text format ;
+| read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]
+| One *validPairs* file is generated per reads chunck. These files are then merged in the *allValidPairs*, and duplicates are removed if specified in the configuration file.
+
 | The contact maps are then available in the *matrix* folder. The *matrix* folder is organized with *raw* and *iced* contact maps for all resolutions.
+| Contact maps are stored as a triplet sparse format ;
+| bin_i / bin_j / counts_ij
+| Only no zero values are stored. BED file described the genomic bins are also generated. Note that *abs* and *ord* files are identical in the context of Hi-C data as the contact maps are symmetric.
+
 | Finally, the *pic* folder contains graphical outputs of the quality control checks.
 
 

doc/RESULTS.rst

@@ -30,7 +30,12 @@ List of valid interaction products
 ----------------------------------
 
 | The *hic_results* folder contains all Hi-C processed data, and is further divided in several sub-folders.
+
 | The *hic_results/data* folder is used to store the valid interaction products (*'.validPairs'*), as well as other statisics files.
+| The *validPairs* are stored using a simple tab-delimited text format ;
+| read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]
+| One *validPairs* file is generated per reads chunck. These files are then merged in the *allValidPairs*, and duplicates are removed if specified in the configuration file.
+
 | Statistics about read pairs filtering are available in the *'.RSstat'* files, and combined in the *'SAMPLE_NAME.mRSstat'* file.
 | The ligation efficiency can be assessed using the filtering of valid and invalid pairs. As the ligation is a random process, 25% of each valid ligation class is expected. In the same way, a high level of dangling-end or self-circle read pairs is associated with a low quality experiment, and reveals a problem during the digestion, fill-in or ligation steps. 
 | In the context of Hi-C protocol without restriction enzyme, this analysis step is skipped. The aligned pairs are therefore directly used to generate the contact maps. A filter of the short range contact (typically <1kb) is recommanded as this pairs are likely to be self ligation products.
@@ -69,7 +74,7 @@ Intra and inter-chromosomal contact maps
    (...)
 
 
-This format is memory efficient, and is compatible with other analysis softwares such as the `HiTC Bioconductor package <http://bioconductor.org/packages/release/bioc/html/HiTC.html>`_.
+This format is memory efficient, and is compatible with other analysis softwares such as the `HiTC Bioconductor package <http://bioconductor.org/packages/release/bioc/html/HiTC.html>`_ or the `HiCPlotter software <https://github.com/kcakdemir/HiCPlotter>`_.