flip mate-pair libraries from rf to fr

Question

[Damian Kao]

Are there any existing tools to artificially flip mate-pair libraries from rf to fr?

Edit

I really just need to reverse complement both libraries to make it fr right? fastx toolkit has a reverse-complement tool. I am trying that out now.

[Ashutosh Pandey]

Just curious, are these lexogen libraries that generate reads in a strand orientation opposite to the genomic reference?

Answer 1

[Biomonika (Noolean)]

Correct, you only need to reverse complement all of your reads.

Answer 2

[oranzus90]

Should I only RC one strand?

When I RC both of the strands and than use Tophat on them, I get unwanted results.

[Brian Bushnell]

Depends on your library type. What is the orientation?