Quality not looking good demux-paired

Hi all,
My recent sequencing result look something like this (attached figure). I normally do whatever I have been doing, followed the same protocol. Does anyone have any perception on
demux-paired-end-durpbulkchem.qzv (313.3 KB)
why my quality looks like this? Should I redo my sample?

Any help is very much appreciated !!

Sincerely ,

Looks like R2 failed to sequence well.

If you have access to the Illumina quality report from the run, this could show you over/under clustering. (Not the q-score graph, but the health checks from the instrument itself.)

If it's your machine, you could ask Illumina to send you a new flow cell if something went wrong.

Unfortunately, resequencing is probably needed to get good data from R2.

Fortunately, R1 looks good so you could put that through DADA2 denoise single!

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thank you Colin, I am waiting for report. Will tag you back once I get it.

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Please find the attached pic

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>=q30 = 42.7%
Clusters passing filter 2.4%

Yeah, that explains it.

I'm not an expert on sequencing so I'll offer no advice, other than to try DADA2 on your R1 data.

Let us know what you try next!

Any ideas if this is sequencing error or machine error or my samples are not good?

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Thank you for your patience, Parikrama,

I did notice something on the reverse read.
(We usually called forward R1 and reverse R2, but they call the two index reads R2 and R3, so the reverse read becomes R4.)

The quality for R2 a.k.a R4 is really low. Having only 10.83 %> Q30 is much lower compared to the forward read.

I also asked a college of mine, but I have not heard back yet.
I'll post again if I hear back! :postbox:

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