Hello, I'm new to Illumina. I got my sequences back from sequencing center. I did 16S rRNA amplicon sequencing with paired-ends MiSeq 2X300bp. I have 10 samples totally. I got two fastq files back. One is forward total (10sample) reads, the other is the reversed reads.
1> I checked my raw fastq files ( forward and reverse ).Reads in the files begin with barcode (8bp) + primer (20bp). This means my primers are still in the sequences.
2> Also, another thing that I don't understand. I think forwards reads should be sequenced by forward primer, and reverse reads should be sequenced by reversed primer. It is interesting both forward and reverse reads are sequenced by forward primer? (Only forward primer sequences in them, Is this possible?) Both forward and reverse reads at the beginning of each read are 8bp barcode+ 20bp forward primers.
I thought revered reads should be 8bp barcode + reversed primer and this should be at the end of each reads? Did sequencing center sort the direction for me?
3> Also, I don't understand this. When illumina does the actually sequencing? For WGS, it uses universal primers right? How about amplicon? does it use universal primers or the PCR primers.
Thanks,
1> I checked my raw fastq files ( forward and reverse ).Reads in the files begin with barcode (8bp) + primer (20bp). This means my primers are still in the sequences.
2> Also, another thing that I don't understand. I think forwards reads should be sequenced by forward primer, and reverse reads should be sequenced by reversed primer. It is interesting both forward and reverse reads are sequenced by forward primer? (Only forward primer sequences in them, Is this possible?) Both forward and reverse reads at the beginning of each read are 8bp barcode+ 20bp forward primers.
I thought revered reads should be 8bp barcode + reversed primer and this should be at the end of each reads? Did sequencing center sort the direction for me?
3> Also, I don't understand this. When illumina does the actually sequencing? For WGS, it uses universal primers right? How about amplicon? does it use universal primers or the PCR primers.
Thanks,
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