how to choose cufflinks library type from infer_experiment
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
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In second case that looks like an unstranded library.
So, for the first case the answer would be
fr-firststrand, while for the second it would befr-unstranded?That is correct.