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
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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:
Thank you so much for your help, it worked
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