# Differences in representative sequences between QIIME1 and QIIME2

**URL:** https://forum.qiime2.org/t/differences-in-representative-sequences-between-qiime1-and-qiime2/6812
**Category:** User Support
**Created:** [November 6, 2018, 12:54pm UTC](https://forum.qiime2.org/t/differences-in-representative-sequences-between-qiime1-and-qiime2/6812 "2018-11-06T12:54:53Z")
**Posts on this page:** 1
**Showing post:** 23

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### Author: ![cdeai](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/c/a3d4f5/32.png) [@cdeai](https://forum.qiime2.org/u/cdeai)
#### Post date: [November 15, 2018, 1:55pm UTC](https://forum.qiime2.org/t/differences-in-representative-sequences-between-qiime1-and-qiime2/6812/23 "2018-11-15T13:55:31Z")

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Thanks!

I checked back to my logs and I did actually attempt to do the chimera filtering step in QIIME1, but it removed no sequences.

So, reading on a similar problem ([Many chimeric reads after dada2, but only in some samples - #7 by Mehrbod\_Estaki](https://forum.qiime2.org/t/many-chimeric-reads-after-dada2-but-only-in-some-samples/4299/7)) I understand that all of the above means, that the large portion of the chimera sequences is "real" (i.e. arising in the amplicon preparation step, possibly due to low amount of template DNA we were working with) and not a problem with the sequencing or analysis. In other words, it is safe to assume that the sequences that are removed, _should_ be removed and that this improves the result rather than introduce bias to it. The reasonable solution in this case is therefore to use the single-end dada2 protocol.

In any case most samples look much better now, so single-end seems to be the way to go. Am I right?

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