I have been running featureCounts to count mapped reads in RNA-Seq paired-end data with the following parameters
featureCounts -T 10 -t exon -s 2 -p -g gene_id -a <path_to_annotation.gtf> -o <path_to_outoput_directory> mapped.bam
as mentioned in http://bioinf.wehi.edu.au/featureCounts/
However, I came across two posts where the parameters
- --primary https://bioinformatics-core-shared-training.github.io/CRUK_CI_RNAseq_course/Supplementary_Materials/S2_Read_Counts_with_Subread.html
- --largestOverlap How to calculate distribution of mapped read over classes of RNA?
have been used.
This got me a little confused and will like to to know if and when I should use these parameters as well as what will be the difference in the output from the default parameters?
Many thanks in advance