Hello,

I am checking the strandness of a sample using infer_experiment.py and I got a pretty confusing result (for me).

infer_experiment.py -i sample_Aligned.sortedByCoord.out.bam -r gencode.v36.annotation.gene.bed

Results in:

This is PairEnd Data
Fraction of reads failed to determine: 0.4848
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0122
Fraction of reads explained by "1+-,1-+,2++,2--": 0.5030

So half fails to be determined and half seems to be strand-specific.

I know where this sample comes from, so I know that it's a strand-specific library. My question is why do I have half of the reads undetermined?

Any ideas?