I have multiple paired-end bam files from rnaseq experiments (hisat2 aligned). I extracted properly-paired reads, sorted, indexed and ran featureCounts using the following command (as per http://bioinf.wehi.edu.au/featureCounts/):
featureCounts -p -t exon -g gene_id -a species.gtf -o bam.featureCounts *.bam
While it is still running, I can see the following in the log file:
|| Threads : 1 || || Level : meta-feature level || || Paired-end : yes || || Strand specific : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || || Chimeric reads : counted || || Both ends mapped : not required ||
I am confused regarding whether I should count
multimapping reads or not and how it would effect the differential gene expression analysis? I have gone through A: Dealing with multimapping reads in featureCounts post, but would like to know more opinion.
Also the userguide says: "Due to the mapping ambiguity, it is recommended that multi-mapping reads should be excluded from read counting (default behavior of featureCounts program) to produce as accurate counts as possible."