Importing FASTA

Hello,
First, thank you for this amazing community.

I received a ZIP archive of sequence(FASTA) files for each sample after pre-processing ,i.e. read merging, adapter&quality trimming, and chimeric checking.
I want to import these files to qiime2 and perform an analysis with Deblur and feature table construction.
Can you please help me understand how this is done? I couldn't find a solution in the import manual.

Thank you,
Lena

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Have you tried converting them to fastq?

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May be this will help
https://docs.qiime2.org/2020.6/tutorials/importing/#sequences-without-quality-information-i-e-fasta

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Hi @LenaLapidot,

I think @steffi has provided wonderful advice, but I want to re-iterate @Angelica’s question, because deblur needs sequences with quality in QIIME 2. (edit: The amazing @Nicholas_Bokulich pointed out that you can denoise using just vanilla deblur without quality scores.)
You could also still do OTU clustering in QIIME.

Best,
Justine

Unfortunately I don’t have the quality scores…

Thank you, that was the plan, however I have multiple FASTA files - each sample has a separate FASTA file, so I have to covert them all to sequences.fna first…
Do you have a suggestion ?

Thank you :slight_smile:

Perfect! Thank you for this important advise :slight_smile:

How can I do the vanilla Deblur without the quality scores?

Hi @LenaLapidot,

I haven’t done it recently, but I think if you run the command deblur on your terminal, you’ll get help documentation. You could. also check the github page.

Best,
Justine

Hi @LenaLapidot

Yeah. I think you to convert your fastq files into sequence.fna and then upload. U can achieve this using qiime1. http://qiime.org/tutorials/processing_illumina_data.html.
As far as I know, We can do this in qiime2 pipeline. Correct me if I am wrong

Updating that I’ve installed deblur (conda) and the Deblur command worked :slight_smile: Now I am trying to continue with qiime2 analysis, mainly for the tree and taxonomy. If there’s anything I should pay attention to, please let me know. Thank you for the help and the support!

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Thank you, Steffi! I’ve done this with the split libraries command. However, it looks that I have to continue with OTU clustering… so now I’m trying to go with the “vanilla” Deblur option.

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Hi,
I am not familiar with vanila Deblur option. Its good that you found a way to go ahead.

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Hi @LenaLapidot,

At thsi point, I’d go forward with your favorite tree building and taxonomy assignmeent algorithm. I think the tutorials give a nice set of options.

Best,
Jusitne

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