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Old 11-27-2018, 11:25 AM   #1
Location: MO, USA

Join Date: Apr 2011
Posts: 83
Default Sequencing quality question.


Iím analyzing a metagenomics data set and am a bit concerned about the sequencing quality. It was run using NextSeq for PE150. I need a second opinion. Attached is Mothur's summary.seqs output from one of the samples, Sample10 as an example.

For the raw reads, the max read length is 151, the median is 129.
After assembly (stitch R1/R2 together, max is 292, median is 121.

Almost all the samples are like that more or less. Is this normal or is it an indication of poor seq quality?


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Old 11-27-2018, 08:32 PM   #2
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Location: Eugene, OR

Join Date: May 2013
Posts: 465

It looks like the library fragment length was short, so that many reads have an adapter trimmed off and (I imagine) many of the read 2s completely overlap the R1. What did the library fragment size distribution look like? Do you have trim stats? Or quality stats from the run?
Providing nextRAD genotyping and PacBio sequencing services.
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Old 11-27-2018, 09:22 PM   #3
Jafar Jabbari
Location: Melbourne

Join Date: Jan 2013
Posts: 1,210

As SNPsaurus has mentioned it is more likely library prep issue. Posting FastQC output for raw data would be more informative.
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