amplicon 16S reads qualityc check

Question

[luyang1005]

Hi, community,

I have done my amplicon 16S illumina miseq sequencing. My samples were from wasterwater. However, the raw reads were only around 2000~10000. Is that right?

May I know is there anything wrong with my data?

Thanks in advance.

Answer 1

[lakhujanivijay]

That's strange!

How do you calculate that "2000~10000" ?

[luyang1005]

Hi, 2000~10000 means the raw reads count for each fastq file. But my reads phred score are all above 30. May I know is this right? Thanks.

[lakhujanivijay]

I know thats the number of reads. What I wanted to know is how do you count the number? I want to make sure that there is no mistake in counting; although this is a trivial task.

[luyang1005]

I use the fastqc and do the fastqc, it reported to me the result reads number