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Forum: Illumina/Solexa 08-28-2017, 01:29 PM
Replies: 22
Views: 7,435
Posted By Joanna
Hi guys, I want to post some updates. As...

Hi guys,

I want to post some updates. As people suggested, we ordered fresh primers and made new libraries. Then loaded 6pM with 30% PhiX spike in. And we also doubled the volume of sequencing...
Forum: Illumina/Solexa 07-20-2017, 12:48 PM
Replies: 22
Views: 7,435
Posted By Joanna
Jessica- Thanks so much for your super clear and...

Jessica- Thanks so much for your super clear and logical explanation! I really appreciate your patience and expertise.

I think your comments on low complexity and uneven signals for each base...
Forum: Illumina/Solexa 07-20-2017, 11:09 AM
Replies: 22
Views: 7,435
Posted By Joanna
Jessica- Here's the thumbnails, metrics of a...

Jessica- Here's the thumbnails, metrics of a successful run.
Forum: Illumina/Solexa 07-20-2017, 08:14 AM
Replies: 22
Views: 7,435
Posted By Joanna
Jessica- All the QC and sequencing were done by...

Jessica- All the QC and sequencing were done by the sequencing core. And based on their comments, everything looked fine for them. And I think we had a good communication about using custom primers. ...
Forum: Illumina/Solexa 07-19-2017, 06:03 PM
Replies: 22
Views: 7,435
Posted By Joanna
Yes I agree we can't exclude the possibility of...

Yes I agree we can't exclude the possibility of degradation of our stock primers. We probably still need check that.

I am also attaching the %base vs cycle and DNA assay result. We targeted V3-V4...
Forum: Illumina/Solexa 07-19-2017, 11:38 AM
Replies: 22
Views: 7,435
Posted By Joanna
Hi JoeKutch, Thanks for the comment. I need...

Hi JoeKutch,

Thanks for the comment. I need clarify that we don't have the sequencer. We are working with the sequencing center in our university. They have done the troubleshooting with Illumina...
Forum: Illumina/Solexa 07-19-2017, 10:04 AM
Replies: 22
Views: 7,435
Posted By Joanna
Hi Jessica, Thanks a lot for your advice. ...

Hi Jessica,

Thanks a lot for your advice.
We did change the PCR water and buffer etc. at the first place to make sure there's no contamination. And our primer has i5 and i7 adapters in it, so we...
Forum: Illumina/Solexa 07-19-2017, 06:14 AM
Replies: 22
Views: 7,435
Posted By Joanna
Hi nucacidhunter, Thanks for your reply! We...

Hi nucacidhunter,

Thanks for your reply! We did get much higher PhiX than expected. We thought about low quality so we tried new dilutions from our stock primers and new sequencing primers. All...
Forum: Illumina/Solexa 07-18-2017, 01:29 PM
Replies: 22
Views: 7,435
Posted By Joanna
Question Miseq v2- Low cluster density, Low PF%, what should we do?

Hi everyone,

We have been sequencing bacterial 16S rRNA gene libraires for about 3 years, prepared with custom dual-index primers (not staggered), followed Kozich paper...
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