CODE:

- First mapping. Removed step to produce a filtered map file from the raw map produced by the gemtools rna-pipeline. Now a raw bam is directly produced from the raw map.
- Added a new step to produce a filtered bam file without unmapped reads, multimapped and mapped with more than 4 mismatches. Definition of a multimapped read changed, before considering only the best stratum, now considering the best one and the nearby one. More multimapped reads to remap in the second mapping.
- Extract reads to remap. Done from the raw bam instead of from the raw map. Approach completely different using "bedtools bamtofastq" and free of bugs (before reads with 5 mismatches not remapped by mistake).
- Some little edits in the name of variables and intermediate files.