FR - firststrand meaning

[ttttuck]

Hello, how are you?

Is the option library_type first referred to 1+-,1-+,2++,2--, reads R2 in the same direction as the RNA fragment and mapped to the positive strand?

Considering PE reads and:

Fraction of reads explained by "1++,1--,2+-,2-+": 0.0906
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9073

Thanks in advance,

Tlucky

[shaomingfu]

Apologies for late response.

I'm not sure what "1++,1--,2+-,2-+" exactly mean. The library_type first and library_type second used by Scallop mean the same thing as in TopHat tool, for which more explanations are provided in their documentation: https://ccb.jhu.edu/software/tophat/manual.shtml.

If you run Scallop with --preview option and paste the (first few lines) of the printed log here, I might be able to explain more.

Mingfu