Update README.md

Author: axelcournac

README.md

@@ -63,6 +63,25 @@ When running `hicberg`, there are a handful parameters which are especially impo
 * `--start-stage`: Stage to start the pipeline (fastq, bam, groups, build, stats, rescue, final).
 * `--trim5`: Trim <int> bases from 5' (left) end of each read before alignment (default: 0).
 
+
+### Input Files
+
+Input Hi-C data should be in paired-end data in fastq format. The fastq files can be given in compressed format like .gz. 
+
+The reference genome could be in fasta format or directy the index for bowtie2.
+
+### Output Files
+Several files are generated by hicberg.
+  * `unrescued.pairs.cool`: cool file of the Hi-C contact maps without hicberg reconstruction which correspond to what standard pipelines generate.
+  * `rescued.pairs.cool`: cool file of the Hi-C contact maps with hicberg reconstruction.
+  * if the option `-hcsp' is set to True, process from hicstuff https://github.com/koszullab/hicstuff are also applied like filtering of uncuts, recircularised events.., removal of duplicates. These files contained the extention .filtered (e.g: rescued.pairs.filtered.cool).
+    
+
+
+ The cool format is an efficient and compact format for Hi-C data based on HDF5. It is maintained by the Mirny lab and documented here: https://open2c.github.io/cooler/
+For more informations, see the [cooler documentation](https://cooler.readthedocs.io/en/latest/cli.html#cooler-load)
+
+
 ### <a id="contributing"></a> Contributing
 
 All contributions are welcome, in the form of bug reports, suggestions, documentation or pull requests. We use the Numpy standard for docstrings when documenting functions.