Bad read2 quality in Miseq

[Elham1]

Hi All,

I did the exome enrichment using Illumina platform. I pooled 50 samples in one run. The run went OK but some enriched libraries shown the bad kmer conent and quality score in Read 2. I used the V3 kit, 600 cycles.

I appreciate any kind of suggestion.

[GenoMax]

You should post (I assume FastQC was used) plots instead of just text descriptions so people can see what is going on with your dataset. In general some drop in quality is expected on read 2 but we would need to see an example or two from your dataset.

[Elham1]

Hi All,

I did the exome enrichment using Illumina platform. I pooled 50 samples in one run. The run went OK but some enriched libraries shown the bad kmer conent and quality score in Read 2. I used the V3 kit, 600 cycles.

I appreciate any kind of suggestion.

I upload the plot for read 1 and read 2.

[nucacidhunter]

The Q score plot indicated as R2 looks more like R1 in my experience and is as expected from 2x300 run on MiSeq. R1 scores which could be R2 is little lower than what is expected up to 150 cycle. That could be due to over clustering. I guess you have got over 25 million reads from this run.

The "bad kmer" most likely is relted to capture and may not be a sequencing issue if other samples looks fine.