Metadata sample, IDs types illumina Miseq

Hello everyone

I have the following doubt regarding the metadata file of the sample is as follows:
What is the format my sample metadata should follow if it comes from an analysis of the v-3 v-4 region of RNA16s from four samples that were sequenced with the illumina technology and the Miseq technique the service was performed in Macrogen. The data I received no longer contain the barcodes and I do not find the linker first sequence either.
Can I skip these last two data? and include only the variables that I considered in my study?

Shipping capture of what my Raw data contains

the others are the trimming data

Thank you very much best regards

Good afternoon,

Thank you for posting all your sample names. I think you can import your data into Qiime using the Fastq manifest format. This format only needs file names (it does not need barcodes).

Yes! Only include the sample you want to analize.

I would use the full, raw data files, then do your own trimming and quality filtering in Qiime. The Moving pictures tutorial shows how to do these steps.

Let me know if this helps,
Colin

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Dear @colinbrislawn

Yes, thank you very much

My problem was because basically I create a manifest file however that can not be used as a metadata file (it must be created by ourselves) then.
If I do not have the barcodes or the Linker Primer Sequence, I can create a sample metadate with parameters such as the following:
ID, collection site, forest type, etc.

That is, omitting the sequencing data? That is my great doubt since I am interested in performing alpha and beta diversity analyzes.

Thanks a lot

Hi @Nasute!

No need to worry about that - a manifest file is not the same thing as a metadata file! Manifest files are used for importing per-sample sequences. After you import, that manifest can be trashed. The metadata file is the secret sauce for the rest of your analysis. Check out this tutorial for more details on how to make a metadata file!

That tutorial should help explain what columns you need and don’t need (hint, the only thing you really need is your sample identifiers!).

Take a look at that tutorial and let us know if you have any more questions! Keep on QIIMEing! :t_rex:

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Yes, you will need both a fastq manifest file for importing your data, and a metadata file for “holding ID, collection site, forest type, etc.”

In Qiime 1, these were placed together into a ‘metadata mapping file’. Now, we keep one file for sequencing information…

sample-id,absolute-filepath,direction
RJ8-10,$PWD/some/filepath/RJ8-10_1.fastq.gz,forward
RJ8-10,$PWD/some/filepath/RJ8-10_2.fastq.gz,reverse

and a second file for biological information:

|#SampleID|BodySite|Subject|Timepoint|Description|
|---|---|---|---|---|
|#q2:types|categorical|categorical|numeric|categorical|
|RJ8-10|gut|subject-1|0|RJ8-10|
|RJ8-10|gut|subject-1|2|RJ8-10|

Let me know if you have questions about building a metadata file.

Colin

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@colinbrislawn
That’s right!
It’s clear for me
Thank you very much

@thermokarst
Thank you!
I’m already reviewing the tutorial

Dear @colinbrislawn

try to make a sample metadata that includes only the biological information and try to validate it in Keemei however there are errors because I specify that I have 2 more readings (pairend Foward and Reverse per sample) you know some way to concatenate this information so that you will not believe the program that I am working with different samples?

Attachment screenshot

Hello @Nasute

I think your metadata looks very clear and concise. I see all those duplicates lines too!

Have you imported your data already? I ask because once you have imported your data, one of the next steps will join your paired reads into a single read. For example, the qiime dada2 denoise-paired command in the atacama-soils tutorial will join the forward and reverse reads together.

Exactly! After joining, you will only have one file per sample, so your metadata table will not need to have duplicates.

If you remove the duplicates lines (4,6,8, and 10) in your screenshot, this should work perfectly.

Keep up the good work!
Colin

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