I have dataset composed of 12 samples that were sequenced 150-PE (Pair-End) [Total of 24 files].
I used the collection mode to create a collection of matched pair files.
I uded RNA-STAR - worked great and created the correct BAM files.
Now I would like to use FeatureCounts to have a list gene vs expression.
Everything work wonderful and I have the correct annotation file.
My question is regarding a tab called “Options for paired-end reads”:
In the first line “Count fragments instead of reads”, if you mark “Enabled”, then:
fragments (or templates) will be counted instead of reads.
I tried to find good explanation to what it means to count fragments, what is the algorithm and why it is different from counting reads?
What is the advantage of reading fragments instead of reads if you are using paired-end data?
Thank you in advance.