Checking for strandedness with Infer experiment

Question

[jamesymtang]

Hi all,

When I run Infer experiment on my dual-RNA seq results, I am getting this:

This is PairEnd Data Fraction of reads failed to determine: 0.4012 Fraction of reads explained by "1++,1--,2+-,2-+": 0.5757 Fraction of reads explained by "1+-,1-+,2++,2--": 0.0231

Why is there such a high fraction of reads failed to determine?

I am using KAPA Stranded mRNA-Seq Kit and xGen® Dual Index UMI Adapters on Novaseq 6000 illumina

Also, when I try to do featurecounts using -s1 (Forward stranded) settings, I am not getting any assigned reads.... but with unstranded I do, is there any explanation behind this?

Yours Sincerely, James