Infer experiment - interpret results.

1

Hello,
After using infer experiment, I get the following type of data:
This is PairEnd Data
Fraction of reads failed to determine: 0.4197
Fraction of reads explained by “1++,1–,2±,2-+”: 0.0028
Fraction of reads explained by “1±,1-+,2++,2–”: 0.5775

This means that is reverse stranded data correct?
Also I am using the latest version of the gtf file, why am I still getting 41% failed to determine?

2

Hi @NIKITA_JHAVERI,
yes, you are right. It means that it is reverse stranded. Regarding the fraction of reads that cannot be determined, it may be caused by overlapping gene regions. In order to check it you can have a look at highly expressed genes in IGV. Another possible explanation is a deficient genome annotation.

3

Thank you!

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