Facing problem importing FASTQ file

[Shahariar (Md. Arif Shahariar)]

I am not being able to import my FASTQ data. Can anyone help me by providing the correct command and tutorials? I am a beginner in the field of metagenomics.

[lizgehret]

Hi @Shahariar,

Welcome to the :qiime2: forum!

You'll want to check out the tutorial on Importing Data into QIIME 2 - this will provide you with the requirements for each different input format.

Cheers

[Shahariar (Md. Arif Shahariar)]

I have tried but not getting clear idea about the format and data type. I have shared some picture of the data and error that i encountered during analysis.... Can you give some solution?

[lizgehret]

Hi @Shahariar,

The first input format that you selected was CasavaOneEightSingleLanePerSampleDirFmt, which has the following formatting requirements:

A directory that contains one fastq.gz file for each sample in the study which contains the single-end reads for that sample. The file name includes the sample identifier and should look something like L2S357_15_L001_R1_001.fastq.gz. The underscore-separated fields required in each sample file name are as follows:

• the sample identifier
• the barcode sequence or a barcode identifier
• the lane number
• the direction of the read (i.e. only R1, because these are single-end reads)
• the set number

Your first command didn't work because you provided a fastq file for the input path (rather than a directory containing fastq files) that does not contain the above formatting requirements.

The second format that you selected was SingleEndFastqManifestPhred33, which is one of the FASTQ Manifest formats. These formats expect a manifest file to be given in the input path that contains information regarding the location of all of your FASTQ files, rather than providing the full path to a single FASTQ file (as you did in your command above). Please review the section in the Importing tutorial regarding FASTQ Manifest Formats and how to structure a manifest file.

Did the sequencing center provide you with the format of your FASTQ files (EMP, Casava, etc)? And is the FASTQ file you specified in your commands the only file that you have, or do you have multiple? We'll need more information on your data in order to effectively advise on how you'll import it into QIIME 2.

Cheers