importing data from illumina

Technical Support
1

hi Everyone,

I got 4 files from illumina:
raw_1.fq.gz [Read 1 sequences with barcodes and primers]
raw_2.fq.gz [Read 2 sequences with barcodes and primers]
1.fq.gz [Read 1 sequences with barcode and primer removed]
2.fq.gz [Read 2 sequences with barcode and primer removed]

Could you please answer my two questions?
First is, while importing data on qiime2, should i use the upper two files with primers as the metadata file has the primer column too?
Second is, Should i use the commands related to Casava 1.8 paired-end demultiplexed fastq for importing data on Qiime2?

Thank you in advance

2

Any Help?!!!!!!!???!

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Hi @hadeerismail22,

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Hi @hadeerismail22,

You can use either of the two sets of files, but I would recommend using the bottom two (files with barcodes and primers removed).

You can, but you'll either need to change the names of your files, or create a manifest file for them. Details on the requirements for importing Casava 1.8 paired-end demultiplexed fastq files can be found here, for your reference:
https://docs.qiime2.org/2023.5/tutorials/importing/#casava-1-8-single-end-demultiplexed-fastq

Cheers :lizard:

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Hi @lizgehret,
Thank you so much for your help, it worked

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