I performed RNA-seq analysis on 8 samples(2 control and 6 samples) . I used featureCounts function (Rsubread package) to count the number of reads. I found that Number of assigned reads were very poor. I am attaching the table here for your reference. I have used following function:
fc<- featureCounts(annot$Sample,isPairedEnd=TRUE, GTF.attrType = "transcript_id", annot.ext = "GCF_000203855.3_ASM20385v3_genomic.gtf", nthreads = 3, isGTFAnnotationFile = TRUE)
I do not understand why assignment% is low, when alignment % is found higher. Can anyone help me think of possible reasons for why I'm getting such low values for assignment?
Thanks a lot.