Good afternoon everyone
I am completely new to the bioinformatics of 16s MiSeq paired end data. I have received my data recently. I have a very nice paper explaining what you should do with the data, however I am not sure how to do it in terms of commands. I have 32 samples. I received one large tar.gz file from the sequencing company. Now, I have managed to download the data and extract the files using putty. Currently for each of the 32 samples I have a forward and a reverse fastq.gz file in the Illumina labeling form. I know I have to demultiplex the samples (according to the paper I am reading), but I have no idea what command to use to demultiplex the data. Any help will be appreciated. Hope this information is useful. Once I have demultiplexed the samples and extracted barcodes etc. from the data, I will import the data into QIIME for general 16s analysis.
Regards Sunette
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This thread may help.
Hi @Giovanni.madrigal12
Thank you so much. The only problem I have is, my barcode file is missing, I only received the forward and reverse files, I will see what the sequencing company say about the barcode files, but this is really helpful thank you.
Follow this tutorial on Qiime wesbite: http://qiime.org/tutorials/processing_illumina_data.html and for PE reads, this tutorial would help: https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/qiime-tutorial-3
Hi @cpad0112
Thank you, I will have a look at these. I already also searched on the Qiime website, however, seems like I am missing some files from the sequencing company. The links are really helpful, thank you.