paired/ single- qiita fastq

Hi!
I downloaded preprocessed fastqs. from qiita for example Qiita
i want to do a qiime process on the fastqs, but how can i know the data type, single or paired ? before the process
thanks

Hi @shanif3,
Can you send me a screenshot of the files in your directory?

Also, do you have the metadata associated with these sequences? If so you may be able to find the information you need by looking at the metadata file.

If you havent already, searching the forum for related questions is a great way to find an answer to common issues, have a look through those as well!

-Hannah

Hi @jphagen !
I attached the metadata.
here is a screenshot of the fastq file

thanks!!
10376_prep_1324_20201201-080733 (1).txt (8.4 KB)

Hi @shanif3,

I suspect that these are single end sequences! and I think you should try importing them into qiime as such. You can follow the "Moving Pictures tutorial" or just the importing data tutorial and then check out the other tutorials once you get your data imported and decide what direction you want to take your analysis.
Let me know if you have any questions,
Hannah

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yes i tried to process it as single end sequences and it worked.
but my question is how can i know it for sure?
for a given fastq gz/ metadata how can i know about the data (single vs paired) automaticlly?
thanks!

@shanif3,

I dont believe there is a way to know automatically but if we had been incorrect about your files and they were actually paired-end the import would have given us an error saying so. Its normal to need to look at the data to know what you have, and a little trial and error is normal too! thats science :slight_smile:

-Hannah

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ok, how did you know the type of the data I attached above? what did you look for and where?

thanks!

@shanif3,

In the image you sent me there was only one fastq file. With paired-end sequences there may be two. Also the run prefix in the metadata had _1 which seems to indicated that they are single end. The metadata sometimes will have a column that tells you paired or single as well. I hope this helps!

-Hannah

the image include one gz file- so you consider it as one fastq file?
so basically, if there is no "_2" on the metadata, the fastq is single right?

so if the fastq were paired, how this command would look? (this is for single):
coomand=[
"qiime", "tools", "import",
"--type", "MultiplexedSingleEndBarcodeInSequence",
"--input-path", fastq_path,
"--output-path", multiplexed_qza_file_path
]

one last question, i tried to add to "qiime import" (the one above) --verobse option and it failed, how can i see what's going on behind the scenes?

thanks so much @jphagen !

Hi @shanif3,

Jumping in for @jphagen as she is out for the end of year holidays.

From the screenshot you provided, you can see that there is one FASTQ File (741_seqs.fastq). If that is all that was contained within the gz file (which looks like is the case), then yes, there is only one FASTQ file within the zipped archive.

Not necessarily. Typically, with paired end sequence data you'll have two files (one for the forward reads and one for the reverse reads). The formatting may look different depending on how the sequencing data was processed. Here's an example of what paired end Illumina reads might look like.

Make sure you read through the Importing Data into QIIME 2 tutorial that @jphagen linked in one of her responses above. This goes through importing all of the different types of data and their associated formats - single and paired end imports are discussed in detail.

The --verbose flag isn't available for the import command, as all of the error handling will be directly provided if there are any issues with the import. What's happening behind the scenes is the file provided as input is matched against the provided input type (and the associated file validation checks for that particular type), and is zipped up as a QIIME 2 Artifact if the file matches the type provided.

Cheers :lizard:

1 Like

Thanks @lizgehret ! enjoy the holiday :slight_smile:

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