Amplicon processing

[arkilis]

"By default, amplicon processing discards all reads that fail to reach the reverse primer (using the ShortQuality filter)"

Could anyone explain this in a little bit detail? Thanks!

[JackieBadger]

it means if you do not have all of your amplicon i.e fwd primer---target sequence---rev primer then the sequence is discarded.

[arkilis]

it means if you do not have all of your amplicon i.e fwd primer---target sequence---rev primer then the sequence is discarded.

You means that some amplicon may not complete like the structure in the above image? THX