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!