# How/when to merge replicates
**URL:** https://forum.qiime2.org/t/how-when-to-merge-replicates/12019
**Category:** General Discussion
**Created:** [October 17, 2019, 5:43am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019 "2019-10-17T05:43:06Z")
**Posts on this page:** 15
**Page:** 2
### Author:  [@Nis\_12](https://forum.qiime2.org/u/Nis_12)
#### Post date: [October 31, 2019, 4:47am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/22 "2019-10-31T04:47:37Z")
even i am not able to this steps. i had convert sff file to fastq file and then merged the replicates. then make it as a single file that is casava-18-single end
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### Author:  [@llenzi](https://forum.qiime2.org/u/llenzi)
#### Post date: [October 31, 2019, 10:04am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/23 "2019-10-31T10:04:16Z")
Dear @Nis_12,
sorry to jump in, but I would suggest you to think harder at pro and cons on merging the replicates as you are trying to do. You will have less file to handle at this point, that is only the importing step because after import would not make any real difference, but on the cons side you are loosing the flexibility to investigate if samples replicate behave similarly, ie you wont be able to remove outliers when analysing alpha/beta- diversity. So it is worthy to make your life easy now but potentially much harder at analysis time where you want to focus on identify differences among groups?
If you importing with a manifest file, the barcode is not a problem because they won't compare in any file, you can remove them form the metadata file if you have in there because they are simply redundant with the unique sample/group identifier.
Best wishes
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### Author:  [@Nis\_12](https://forum.qiime2.org/u/Nis_12)
#### Post date: [November 4, 2019, 8:15am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/24 "2019-11-04T08:15:55Z")
now again i stuck in this step as i visualize the results it shows like this
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### Author:  [@ben](https://forum.qiime2.org/u/ben)
#### Post date: [November 4, 2019, 3:15pm UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/25 "2019-11-04T15:15:25Z")
go to: [view.qiime2.org](http://view.qiime2.org)
drag the \*.qzv file into the web browser.
You should be able toe. view the demux file that way.
Ben
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### Author:  [@Nis\_12](https://forum.qiime2.org/u/Nis_12)
#### Post date: [November 19, 2019, 6:11am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/26 "2019-11-19T06:11:45Z")
dear ben as i have completed my analysis. as what results are major used for publication and my last question is how to generate alpha rarefration curve through r.
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### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [November 19, 2019, 3:45pm UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/27 "2019-11-19T15:45:36Z")
> [@Nis\_12](#):
>
> i have completed my analysis.
Congratulations! 🏆
> [@Nis\_12](#):
>
> what results are major used for publication
This depends on the biological question. You should talk to your PI about your results and see what they think is most interesting. You can tell us about your biological question too! đź¦
* * *
> [@Nis\_12](#):
>
> how to generate alpha rarefration curve
👉 [“Moving Pictures” tutorial — QIIME 2 2019.10.0 documentation](https://docs.qiime2.org/2019.10/tutorials/moving-pictures/#alpha-rarefaction-plotting)
> [@Nis\_12](#):
>
> how to generate alpha rarefration curve through r
Why do this in R and not Qiime 2?
See the `rarecurve()` function on this page: [An introduction to the downstream analysis with R and phyloseq — micca 1.7.0 documentation](https://micca.readthedocs.io/en/latest/phyloseq.html)
Colin
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### Author:  [@Nis\_12](https://forum.qiime2.org/u/Nis_12)
#### Post date: [November 20, 2019, 9:59am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/28 "2019-11-20T09:59:40Z")
i had generated through qiime2 but that graph is based on only bardode based on sample based. as i want that the curve shows the results on sample-id based not in barcode. here i have attach my result
even i am not able to retrieve the result in svg and png format
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### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [November 20, 2019, 2:19pm UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/29 "2019-11-20T14:19:09Z")
Have you tried changing the value of the Sample Metadata Column drop down box? What other options are in that drop down box, and does it includes sample-id?
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### Author:  [@Nis\_12](https://forum.qiime2.org/u/Nis_12)
#### Post date: [November 21, 2019, 5:25am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/30 "2019-11-21T05:25:08Z")
no there is no option for sample-id.
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### Author:  [@llenzi](https://forum.qiime2.org/u/llenzi)
#### Post date: [November 21, 2019, 9:59am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/32 "2019-11-21T09:59:02Z")
Hi @Nis_12,
yes you are right, the rarefaction plug in exclude the sample-id column from the output.
Now the question is on the metadata file you used, there is any column that contain unique value, that could be used as alternative to sample-id?
An example, if in your metadata you have, eg:
sample-id barcode
sample1 bc1
sample2 bc2
sample3 bc3
In this case, visualising the rarefaction curve using the 'barcode' category in the drop-down list will be the same as using 'sample-id'.
If you have the sample with same barcode (as I suspect because you merged the samples), you probably have to repeat the rarefaction step, adding a further column in the metadata file that reflect the sample-id (the name of the column does not really matter as long as is not reserved, eg, 'unique-id' should work if my memory is not failing me), such as:
sample-id barcode unique-id
sample1 bc1 sample1
sample2 bc2 sample2
After visualising the file, you should be able to switch the plot to visualise the 'unique-id' category.
Luca
PS this is something that happens only with the rarefaction plug-in, because the visualiser for the diversity plug ins will show the data for the 'sample-id' category.
Luca
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### Author:  [@Nis\_12](https://forum.qiime2.org/u/Nis_12)
#### Post date: [November 21, 2019, 11:51am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/33 "2019-11-21T11:51:53Z")
hello @llenzi
Thank you
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### Author:  [@Nis\_12](https://forum.qiime2.org/u/Nis_12)
#### Post date: [November 23, 2019, 5:15am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/34 "2019-11-23T05:15:35Z")
As i am not able understand how could i intrepretate this results.?
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### Author:  [@Nis\_12](https://forum.qiime2.org/u/Nis_12)
#### Post date: [November 23, 2019, 5:19am UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/35 "2019-11-23T05:19:34Z")
as i am finding the transgenic and non transgenic difference between the soil samples...So we have seen the bacterial taxonomy in the soil samples.
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [November 23, 2019, 4:04pm UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/38 "2019-11-23T16:04:31Z")
Hi @Nis_12 - please post any additional questions or requests for support in a new topic, this one is becoming difficult for us to follow and keep track of (usually one "discussion point" per forum topic is best). Thanks!
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [November 23, 2019, 4:04pm UTC](https://forum.qiime2.org/t/how-when-to-merge-replicates/12019/39 "2019-11-23T16:04:39Z")
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