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Forum: Vendor Forum 05-13-2015, 05:26 AM
Replies: 111
Views: 72,858
Posted By rogerzzw
BTW, Kentawan Another lab using the same...

BTW, Kentawan

Another lab using the same kit and protocol do not have this kind issue at all, which makes me very confusion.
Forum: Vendor Forum 05-13-2015, 04:55 AM
Replies: 111
Views: 72,858
Posted By rogerzzw
@Kentawan Hi, Kentawan we used Kapa...

@Kentawan

Hi, Kentawan

we used Kapa quantification kit, too. and we applied very strict quantification. We quantified individual library concentration firstly and pooled them together based on...
Forum: Vendor Forum 05-12-2015, 12:12 PM
Replies: 111
Views: 72,858
Posted By rogerzzw
@Brian Bushnell Illumina said it is very...

@Brian Bushnell

Illumina said it is very normal by looking the flowcell and other metrics.
Forum: Vendor Forum 05-12-2015, 12:07 PM
Replies: 111
Views: 72,858
Posted By rogerzzw
I have no idea what might cause it.........

I have no idea what might cause it...... consistently.
Forum: Vendor Forum 05-12-2015, 11:51 AM
Replies: 111
Views: 72,858
Posted By rogerzzw
@GenoMax if it is library issue, 60-70% are...

@GenoMax

if it is library issue, 60-70% are demultiplexed very well, I cannot explain that.
Forum: Vendor Forum 05-12-2015, 11:45 AM
Replies: 111
Views: 72,858
Posted By rogerzzw
Yes, those 4 Chip-seq samples barcodes are well...

Yes, those 4 Chip-seq samples barcodes are well selected. But, the problem is I am not sure if it is due to low diversity since it is highly diverse when we combine chip-seq samples. It was still...
Forum: Vendor Forum 05-12-2015, 09:50 AM
Replies: 111
Views: 72,858
Posted By rogerzzw
Hi, Kentawan. I am a beginner of NGS on...

Hi, Kentawan.

I am a beginner of NGS on Nextseq 500. I am primarily doing whole genome bisulfite sequencing with Nextseq 500. I saw your post on this forum and would like to learn from you.
...
Forum: Illumina/Solexa 05-05-2015, 10:17 AM
Replies: 8
Views: 2,588
Posted By rogerzzw
The barcodes I am using is 1. AGTGAG and...

The barcodes I am using is
1. AGTGAG and GCACTA
2. AGTGAG and TGGTGA

But there are other groups suggesting they have no issue on barcodes, which makes me even more confused.

Thanks
Forum: Illumina/Solexa 05-05-2015, 10:12 AM
Replies: 8
Views: 2,588
Posted By rogerzzw
Hi, Phillip. I am always using 2 samples. I...

Hi, Phillip.

I am always using 2 samples. I will use only one sample for next run to see what happens. We are doing 150bp PE
Forum: Vendor Forum 05-05-2015, 09:33 AM
Replies: 111
Views: 72,858
Posted By rogerzzw
We always use V2. Our machine is brand new,...

We always use V2.

Our machine is brand new, and it had a good 1st run only on Phix. Then I started to see the tag reading problem for 4 times.

Once comparing with other people's method of...
Forum: Vendor Forum 05-05-2015, 09:22 AM
Replies: 111
Views: 72,858
Posted By rogerzzw
Hi, GenoMax I talked to tech support. We...

Hi, GenoMax

I talked to tech support. We loaded as suggested (1.8pM - 2pM), but our cluster density is always lower than expect( ~140k/mm2 vs ~200k/mm2).

I learnt from several posts that the...
Forum: Vendor Forum 05-05-2015, 09:09 AM
Replies: 111
Views: 72,858
Posted By rogerzzw
WGBS poor index and read2 on Nextseq

Hi, Guys

I am new to NGS. We've been trying to do whole genome bisulfite sequencing with Nugen Kit on Nextseq 500 for a few times with 2 samples.

We always encountered the same problem. After...
Forum: Illumina/Solexa 05-05-2015, 06:59 AM
Replies: 8
Views: 2,588
Posted By rogerzzw
partial poor quality index and read2

Hi, Guys

I am new to NGS. We've been trying to do whole genome bisulfite sequencing on Nextseq 500 for a few times with 2 samples.

We always encountered the same problem. After demultiplexing,...
Forum: Illumina/Solexa 03-12-2015, 06:14 PM
Replies: 5
Views: 2,067
Posted By rogerzzw
Have not yet. I used kit that not come from...

Have not yet.

I used kit that not come from illumina.
Forum: Illumina/Solexa 03-12-2015, 04:50 PM
Replies: 5
Views: 2,067
Posted By rogerzzw
Thanks, luc. What we did is pooling several...

Thanks, luc.

What we did is pooling several different libraries (made by two persons) together to get sequence. It turned out about 30% of reads did not match any of the barcodes used in library...
Forum: Illumina/Solexa 03-12-2015, 10:03 AM
Replies: 5
Views: 2,067
Posted By rogerzzw
we had the same problem with 1st run in our lab....

we had the same problem with 1st run in our lab. Do you have a idea what's going on?

Appreciate your help
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