Hello!
I'm writing because I'm new at this and I'm having some difficulty understanding if my files are already demultiplexed or not.
I have 80 fastq files (40 forward + 40 reverse), and inside there are several entries however where the index or barcode should be there is the same number (same for the r1 and respectively r2 file)
and they look like the following:
Hi @Bruna_Rodrigues,
first of all welcome in the forum and happy QIIMING!
How many samples do you have in total?
My best guess is that your data are demultiplexed, one fastq pair for each sample.
What are the filenames? Is there any reference of the sample in the file name?
If the sample id it is not included in the file name, I would expect a table which let you correlate each file pairs to specific sample.
If the fastq are not demultiplexed, you definetly need more information on what barcodes are used for each sample and why you received the data splitted in 40 chunks!
If you are in doubt, I suggest you to contact the sequencing provider, thye should be able to guide you on the fastqs are obtained and how to proceed with them.
Hope it helps
Luca
yeah the file names are in the following format S18-51_1_ITSKYO_R1.fastq, they have the sample number. Thank you for your help! From what you said and what I've seen the data is already demultiplexed. Nevertheless when I can I will check with who provided me the data
Thank you agains 
