DOCUMENTS.

 - Added internal links to subsections.

 - Remarked that the chimeric junctions file is the most important output.

 - In ouput subsection added a link to GEMtools rna-pipeline.

 - System requremnets RAM. ~40G for about 100M PE reads of 52 bp.

 - Changed "similarity between gene pairs text file" by "gene pair similarity file".

 - In manual, input and Paired-end (PE) RNA-seq reads  subsection move the less important info to FAQS.

 - In manual, input and Similarity between gene pairs (Optional) explanation. Move the big explanation about how the file is produced to FAQS.

- In mandatory arguments , move -e|--sample-id to optional args. -e|--sample-id sample1 – Sample identifier (the output files will be named according to this id).
Merge branch 'master' of github.com:brguez/ChimPipe