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flip mate-pair libraries from rf to fr

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.

mate-pair
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updated by Ram Ram • written by Damian Kao Damian Kao

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

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updated by Ram Ram • written by Ashutosh Pandey Ashutosh Pandey

2 answers

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

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written by Biomonika (Noolean) Biomonika (Noolean)

Should I only RC one strand?

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

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written by oranzus90 • oranzus90

Depends on your library type. What is the orientation?

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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

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