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Forum: Illumina/Solexa 01-10-2017, 12:33 PM
Replies: 68
Views: 22,729
Posted By d00b
you can mix multiple amplicons

Hi Jin,

we do run multiple amplicons that labeled with different index primers.
However, we do always see index contamination in very low level.

We do two step library preparation.
1)...
Forum: Illumina/Solexa 03-03-2016, 12:56 PM
Replies: 6
Views: 2,749
Posted By d00b
V3 600 cycles kit's Q score issue has been well...

V3 600 cycles kit's Q score issue has been well noticed.
However, our low Q score issue was also related with focusing problem.
Our normal Q score with V3 600 is over 70% as illumina spec....
Forum: Illumina/Solexa 03-03-2016, 10:38 AM
Replies: 6
Views: 2,749
Posted By d00b
We have MCS 2.5.05. Yes, we have contacted...

We have MCS 2.5.05.
Yes, we have contacted them several times and we are still waiting for their review on this run. Do you have same issue with MCS V.2.6.x? Would you share your experience?
...
Forum: Illumina/Solexa 03-03-2016, 09:45 AM
Replies: 6
Views: 2,749
Posted By d00b
"Out of focus" on Miseq cluster

Hi Miseq users,

We have low Q score issue with Miseq V3 600 cycles kit.
Cluster density was ~1000K, PhiX was ~5% aligned and PF was higher than 87.8%.

Based on illumina spec, we supposed to...
Forum: Illumina/Solexa 02-23-2016, 08:27 AM
Replies: 68
Views: 22,729
Posted By d00b
Dear Ksawatzki, Many peoples are complaining...

Dear Ksawatzki,

Many peoples are complaining V3 kit issue.
Many seq core facilities are refusing V3.

Read these articles from everywhere.


Insight into biases and sequencing errors for...
Forum: Illumina/Solexa 12-29-2015, 03:05 AM
Replies: 68
Views: 22,729
Posted By d00b
V2 kit is better than V3

Qscore dropping

http://postimg.org/image/zfwnk5r6n/
Forum: Ion Torrent 10-29-2015, 12:48 PM
Replies: 21
Views: 23,923
Posted By d00b
homemade magnetic stand for amplicon purification

http://i64.tinypic.com/246neqa.jpg
Forum: Illumina/Solexa 05-11-2015, 09:30 AM
Replies: 3
Views: 1,723
Posted By d00b
Thank you so much. We just received another miseq...

Thank you so much. We just received another miseq new machine and we have a plan to compare two machines. After the lower Q30 with newer lot of V2 kit, every things are being skeptical.
Forum: Ion Torrent 05-10-2015, 05:18 PM
Replies: 121
Views: 105,059
Posted By d00b
Hi tracer, You are using PGM for bacterial...

Hi tracer,

You are using PGM for bacterial identification? which gene target are you using? Are you using non-16S gene as well? or you using 16S with different V regions? what is your primer set...
Forum: Illumina/Solexa 05-10-2015, 05:05 PM
Replies: 3
Views: 1,723
Posted By d00b
Miseq A base intensity signal is decreasing after 100cycles

After 100 cycles, A base intensity is drastically decreasing than other bases.
Is this chemistry issue? or optic issue? Miseq V2 500 cycles kit.
cluster denstiy 850-950 K/mm2.. PF is good.. Q30 is...
Forum: Illumina/Solexa 01-20-2015, 09:36 PM
Replies: 24
Views: 8,269
Posted By d00b
we used exactly same PAL (stopped running) for...

we used exactly same PAL (stopped running) for next new running and it works well. This indicates the PAL is not a problem. it is fluidics.. illumina techsupport said "Miseq should have alert before...
Forum: Illumina/Solexa 01-20-2015, 09:20 PM
Replies: 14
Views: 5,509
Posted By d00b
To Hongjae I see. then your issue is very...

To Hongjae

I see. then your issue is very simple. Just clean up your flow cell and check the gasket surface. you also need to clean the injector nozzle part (orange color) and flow cell holder...
Forum: Illumina/Solexa 01-20-2015, 08:45 PM
Replies: 14
Views: 5,509
Posted By d00b
do you have kakao id? i'd like to call you. thanks

do you have kakao id? i'd like to call you. thanks
Forum: Illumina/Solexa 01-12-2015, 06:27 PM
Replies: 24
Views: 8,269
Posted By d00b
Your flowcell problem

This is flowcell issue. the inlet of the gasket was not well aligned to the injector port. it will make this kind of error. you need to request replacement for the reaction kit and other supply...
Forum: Illumina/Solexa 01-11-2015, 01:23 AM
Replies: 14
Views: 5,509
Posted By d00b
Miseq flowcell bubble and gasket

Miseq flowcell defective gasket causes premature running stop
http://www.imagesup.net/?di=514209720582
Forum: Metagenomics 07-03-2014, 03:59 PM
Replies: 12
Views: 10,365
Posted By d00b
hi Richrr, you switched to a different protocol...

hi Richrr, you switched to a different protocol which is suggested by illumina. do have any information on the new protocol? any website link for the protocol? Thanks
Forum: Illumina/Solexa 09-07-2013, 11:48 PM
Replies: 0
Views: 2,728
Posted By d00b
Counting Uncountable (bias or contamination)

NGS brings many beneficial feature on microbial ecological studies.
16S or 18S diversity by many different NGS platforms.
Microbial ecologist always considers on real vs theoretical after indirect...
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