Hi Users

How do I process paired reads from an Ilumina Miseq platform? If I first
use "Groomer" and then "Filter by quality", the paired reads get out of
sync. I read some responses to similar questions in this Forum  that the
paired reads must first be "joined"  before filtering and then split for
mapping. There is also a "Fastq interlacer" command to join reads. However,
I also read in the Forum that Galaxy requires the filtered paired reads to
be of equal length. But would not the filtering process on the joined reads
also modify the length of each differently? Or can the  NGS: Picard command
"Paired Read Mate Fixer"  be used to re-synchronize the paired reads?

If there is no way around the  requirement for equal lengths, then I guess
that it is really not possible to process paired reads in Galaxy?  But I am
sure it is just my stupidity.

Full disclosure: Be kind, I am a novice in this field, just learning Galaxy
(which by the way is a fantastic resource!).

Larry Simpson
UCLA
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