Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode

Question

[dllopezr]

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?

Answer 1

[Carlo Yague]

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.

[dllopezr]

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

[Carlo Yague]

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