Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
1
2
Entering edit mode
6.6 years ago
dllopezr ▴ 130

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?

trimmomatic paired-end • 13k views
ADD COMMENT
0
Entering edit mode

can we not mention unpaired ? i have a reverse read file that needs a lot of trimming but forward file is usable. I don't understand how to go about it

ADD REPLY
3
Entering edit mode
6.6 years ago

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 COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2682 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6