NCBI File analysis

Hello Team,
I am starting my research of Master in Environmental Science and Technology. I need to carry out analysis of readings made available in the NCBI. I’m trying to make the prediction through PiCrust. I looked for several tutorials on this subject. I have not found any tutotial that analyzes the 16s Illumina files from NCBI, these files are in fastaq format, unique file. Can you help me?

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Hello Engo! Welcome to the Qiime 2! :qiime2:

As you have already looks for tutorials, you have probably found this tutorial about running Picrust in Qiime 2: q2 picrust2 Tutorial · picrust/picrust2 Wiki · GitHub

You can import the fastq files you received from NCBI using the fastq-manifest-format.

Let us know if you have any questions,
Colin

P.S. And if this is your first time using Qiime 2, check out this excellent tutorial:
https://docs.qiime2.org/2019.1/tutorials/moving-pictures/

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Thanks Colinbrislawn !
i´ll try!

Hi Colinbrislawm,

I tried to do as you passed me, but I’m having this error:
(qiime2-2019.1) [[email protected] testeqiimedir]$ qiime tools import --type ‘SampleData[SequencesWithQuality]’ --input-path ManifestFile --output-path single-end-demux.qza --input-format SingleEndFastqManifestPhred64V2
/bin/sh: Symbol `rl_readline_state’ has different size in shared object, consider re-linking
Traceback (most recent call last):
*** File “/home/rafael/dados/Miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/util.py”, line 91, in parse_format***
*** format_record = pm.formats[format_str]***
KeyError: 'SingleEndFastqManifestPhred64V2’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
*** File “/home/rafael/dados/Miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/tools.py”, line 146, in import_data***
*** view_type=input_format)***
*** File “/home/rafael/dados/Miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 206, in import_data***
*** view_type = qiime2.sdk.parse_format(view_type)***
*** File “/home/rafael/dados/Miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/util.py”, line 93, in parse_format***
*** raise TypeError(“No format: %s” % format_str)***
TypeError: No format: SingleEndFastqManifestPhred64V2

An unexpected error has occurred:

*** No format: SingleEndFastqManifestPhred64V2***

See above for debug info.

I downloaded my files from NCBI and extracted the FASTQ through the NCBI toolkit.
link to my .sra
https://www.ncbi.nlm.nih.gov/sra/SRX3151516[accn]

Can u help me ?

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The issue is that you have QIIME 2 version 2019.1 installed, but are following the instructions for version 2019.4 (in which new manifest formats have been introduced and are used in the tutorial).

You have two choices:

  1. Follow the 2019.1 documentation (the link @colinbrislawn provided above will direct you to the older documentation)
  2. install the latest version of QIIME 2 and use the latest documentation (what you used in your command)

Good luck!

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