Question: low assignment reads % in RNA-seq
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parinv • 30 wrote:
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 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. Parin
check if multi-mapped reads are counted or not and use correct strandedness. Talk to the core and check if ribodepletion worked for all the samples.
can you post the alignment summary metrics for example like this