Question

flip mate-pair libraries from rf to fr

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9.8 years ago

Damian Kao 16k

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 • 2.6k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 9.8 years ago by Damian Kao 16k

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

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Ashutosh Pandey 12k

score 0 · Answer 1 · 2015-03-31

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9.7 years ago

Biomonika (Noolean) 3.2k

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

ADD COMMENT • link 9.7 years ago by Biomonika (Noolean) 3.2k

Ram · Answer 2 · 2015-09-21

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9.3 years ago

oranzus90 ▴ 10

Should I only RC one strand?

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

ADD COMMENT • link 9.3 years ago by oranzus90 ▴ 10

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Depends on your library type. What is the orientation?

ADD REPLY • link updated 2.3 years ago by Ram 44k • written 9.3 years ago by Brian Bushnell 20k