Question: amplicon 16S reads qualityc check
0
gravatar for luyang1005
18 months ago by
luyang100520
luyang100520 wrote:

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.

sequence next-gen • 477 views
ADD COMMENTlink modified 18 months ago by lakhujanivijay4.4k • written 18 months ago by luyang100520
0
gravatar for lakhujanivijay
18 months ago by
lakhujanivijay4.4k
India
lakhujanivijay4.4k wrote:

That's strange!

How do you calculate that "2000~10000" ?

ADD COMMENTlink written 18 months ago by lakhujanivijay4.4k

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.

ADD REPLYlink written 18 months ago by luyang100520

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.

ADD REPLYlink written 18 months ago by lakhujanivijay4.4k

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

ADD REPLYlink written 18 months ago by luyang100520
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