how to choose cufflinks library type from infer_experiment

Question

[sgupt46]

Hi, Could someone help me identify the input parameter for cufflinks based on the output of infer_experiemnts.py

This is PairEnd Data
Fraction of reads failed to determine: 0.0896
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0123
Fraction of reads explained by "1+-,1-+,2++,2--": 0.8981

What would be the library type for cufflinks out of the suggested ones

Supported library types:
    ff-firststrand
    ff-secondstrand
    ff-unstranded
    fr-firststrand
    fr-secondstrand
    fr-unstranded (default)
    transfrags

Another dataset has strand info like this, what would be the library type for it?

Fraction of reads failed to determine: 0.0801
Fraction of reads explained by "1++,1--,2+-,2-+": 0.3720
Fraction of reads explained by "1+-,1-+,2++,2--": 0.5479

[GenoMax]

See: RSeQC Output from infer_experiment.py - what does it mean?

In second case that looks like an unstranded library.

[sgupt46]

So, for the first case the answer would be fr-firststrand, while for the second it would be fr-unstranded?

[GenoMax]

That is correct.