Question: Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
0
gravatar for dllopezr
2.6 years ago by
dllopezr60
dllopezr60 wrote:

Hi everyone

I am working with paired-end data in Trimmomatic. This software asks for Forward and Reverse reads and outputs four files: Paired Forward, Unpaired Forward, Paired Reverse and Unpaired Reverse.

¿What is the difference between the Paired and Unpaired files? ¿Which of them I must use for the next analysis?

paired-end trimmomatic • 4.1k views
ADD COMMENTlink modified 2.6 years ago by Carlo Yague5.0k • written 2.6 years ago by dllopezr60
1
gravatar for Carlo Yague
2.6 years ago by
Carlo Yague5.0k
Canada
Carlo Yague5.0k wrote:

After trimming with trimmomatic, some reads can be discared, and their mate become "unpaired". Usually, only a small fraction of the reads become unpaired, and they can be ignored. Alternatively, you can map them as single reads along with the remaining paired reads.

ADD COMMENTlink written 2.6 years ago by Carlo Yague5.0k

Thanks, Carlo. So, in the case when there is not reads discarded ¿There is no difference between paired and unpaired reads?

ADD REPLYlink written 2.6 years ago by dllopezr60
1

When there is no reads discarded, all the reads should remain paired and the unpaired files should be empty.

ADD REPLYlink written 2.6 years ago by Carlo Yague5.0k
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