Trimmomatic : keepBothReads True vs False option

Question

[candida.vaz]

Hello everyone,

Is anyone familiar with the "keepBothReads" in Trimmomatic :

keepBothReads: After read-through has been detected by palindrome mode, and the adapter sequence removed, the reverse read contains the same sequence information as the forward read, albeit in reverse complement. For this reason, the default behaviour is to entirely drop the reverse read. By specifying "true" for this parameter, the reverse read will also be retained, which may be useful e.g. if the downstream tools cannot handle a combination of paired and unpaired reads

I was wondering if the keepBothReads: "True" option is better than using the default "False" option

• First, I'm using STAR aligner and Tophat2 for mapping
• Second, Will there be any compromise in the downstream quantification (by Htseq-count or Cufflinks) if I choose to use "True" and keep both the reads?

Thanks for your time and concern!

Answer 1

[Brian Bushnell]

Dropping one read of a pair leaves you with some read pairs and some singletons, which is generally annoying to deal with, so it's better to keep both when they are perfectly good quality-wise. Alternatively, merging the reads so that the singletons represent the consensus of the pair is another good solution. Just dropping one at random is not usually ideal.

[BioinfGuru]

Dropping reads for any other reason than quality ... is a great way to ruin your data set.