- added new script
SCRIPTS/make_ref.pyto build references from multiple source (gencode, ensembl, refseq). See wiki page Creating a manual reference.
- added new statistics in logs created by
SCRIPTS/count.pyto visualize the number of reads aligned on too many transcripts and reads containing too many mismatches.
- added logs in many secondary analysis scripts.
- fixed multiqc reports when analyzing a high number of sample (many plates).
- made the new
SCRIPTS/make_multiplates_configscript backward compatible with ancient configuration files.
- fixed bug in README files.