# Illumina demultiplexed data with inline index sequences (index5+index7)

**URL:** https://forum.qiime2.org/t/illumina-demultiplexed-data-with-inline-index-sequences-index5-index7/13019
**Category:** User Support
**Tags:** demux, trim
**Created:** [December 30, 2019, 3:49pm UTC](https://forum.qiime2.org/t/illumina-demultiplexed-data-with-inline-index-sequences-index5-index7/13019 "2019-12-30T15:49:33Z")
**Posts on this page:** 1
**Showing post:** 5

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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [January 14, 2020, 3:13am UTC](https://forum.qiime2.org/t/illumina-demultiplexed-data-with-inline-index-sequences-index5-index7/13019/5 "2020-01-14T03:13:08Z")

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What sequencing platform did you use? See here:

> [@Odd display of demux plot](https://forum.qiime2.org/t/odd-display-of-demux-plot/13113/3):
>
> Thanks for the welcome! Only a few QC steps were performed by the sequencing company, including throwing reads with too much adapter contamination. I don't think this is the issue. I've confirmed that our reads were sequenced with a Novaseq and indeed have only 4 quality scores, 2, 11, 25, 37. I've come across [this issue](https://github.com/benjjneb/dada2/issues/791) raised on GitHub. @benjjneb recommends enforcing monotonicity in the fitted error model by changing the error model matrix. I can comprehend how to do this in R, but I am…

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