# Reverse reads - quality plot question
**URL:** https://forum.qiime2.org/t/reverse-reads-quality-plot-question/4062
**Category:** User Support
**Created:** [May 7, 2018, 10:37pm UTC](https://forum.qiime2.org/t/reverse-reads-quality-plot-question/4062 "2018-05-07T22:37:07Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@fstudart](https://forum.qiime2.org/u/fstudart)
#### Post date: [May 7, 2018, 10:37pm UTC](https://forum.qiime2.org/t/reverse-reads-quality-plot-question/4062/1 "2018-05-07T22:37:07Z")
Hi Everyone,
I'm analyzing a new dataset, and, after importing the data into Qiime2 I saw that the quality plot of my reverse reads drops to almost zero and, afterwards, increases.
I'm just wondering why this happened. When I denoise the data (using DADA2), should I trim the reverse reads necessarily up to 180 bp?
Thanks very much,
FS
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### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [May 8, 2018, 6:23am UTC](https://forum.qiime2.org/t/reverse-reads-quality-plot-question/4062/2 "2018-05-08T06:23:02Z")
Hello Fernando,
Yes, trimming at 180 would probably be your best option. Your second best option would be to contact your sequencing center, report this as a failed run, and ask them to run it again. It's possible (hopefully!) that this is some sort of software error and your run is OK, but if I saw that graph, I would see if they could rerun those samples. 😥
Let's see what the dada2 folks recommend.
Colin
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### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [May 8, 2018, 3:22pm UTC](https://forum.qiime2.org/t/reverse-reads-quality-plot-question/4062/3 "2018-05-08T15:22:54Z")
I agree with @colinbrislawn, sorry about your data @fstudart ☹
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### Author:  [@fstudart](https://forum.qiime2.org/u/fstudart)
#### Post date: [May 8, 2018, 6:00pm UTC](https://forum.qiime2.org/t/reverse-reads-quality-plot-question/4062/4 "2018-05-08T18:00:04Z")
Hi Dr. Colin,
Thanks for your feedback. I'm also including the forward plot for your analysis, and I did not see the same artifact with these reads. So, may I assume that this sequencing problem was limited to the reverse reads? Also, when I merge the reads and considering that to merge is only necessary a 20-bp overlap, by trimming the reverse reads up to 180 bp, would it be ok to proceed?
Thanks,
Fernando Studart
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### Author:  [@fstudart](https://forum.qiime2.org/u/fstudart)
#### Post date: [May 8, 2018, 6:02pm UTC](https://forum.qiime2.org/t/reverse-reads-quality-plot-question/4062/5 "2018-05-08T18:02:50Z")
Hi Dr. Bolyen,
Thanks for your reply. I just included the forward plot as well. Do you think I can proceed analyzing this run, as I did not see the same artifact with the forward reads?
Thanks,
FS
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### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [May 8, 2018, 9:41pm UTC](https://forum.qiime2.org/t/reverse-reads-quality-plot-question/4062/6 "2018-05-08T21:41:30Z")
Hello again,
> [@fstudart](#):
>
> So, may I assume that this sequencing problem was limited to the reverse reads?
Yes, that sounds right. And it's common for Illumina data to have issues with one direction.
> [@fstudart](#):
>
> Also, when I merge the reads and considering that to merge is only necessary a 20-bp overlap, by trimming the reverse reads up to 180 bp, would it be ok to proceed?
Yes! This is why paired end reads are soon good! I think your analysis will not even be effected by this region.
Good luck!
Colin
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [June 9, 2018, 3:41am UTC](https://forum.qiime2.org/t/reverse-reads-quality-plot-question/4062/7 "2018-06-09T03:41:34Z")
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