Merge pull request #442 from nschcolnicov/issue_94

Added info about read number behavior

docs/output.md

@@ -195,6 +195,8 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
 
+- Note: There may be a discrepancy in read counts number displayed in MultiQC between the original FASTQ and BAM files, this is due to secondary alignments being reported by the aligner, which can inflate the total read count number in the BAM files. [More info about this behavior can be found here](https://github.com/nf-core/smrnaseq/issues/94).
+
 ### Pipeline information
 
 <details markdown="1">