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Search: Posts Made By: kentawan
Forum: Vendor Forum 05-12-2015, 05:56 PM
Replies: 108
Views: 62,434
Posted By kentawan
Hi Roger, We spiked in a good 20% freshly...

Hi Roger,

We spiked in a good 20% freshly diluted PhiX library, as our library's first 6 bases are the same due to restriction enzyme processing.

As for your question 1, I'd like to know how...
Forum: Vendor Forum 05-12-2015, 05:50 PM
Replies: 108
Views: 62,434
Posted By kentawan
I agreed. We wrote a feedback email to their...

I agreed. We wrote a feedback email to their engineering team too. As you might have expected, it is a disappointing email. Lesson learnt, don't buy too many kits in one shot.
Forum: Vendor Forum 05-07-2015, 10:27 PM
Replies: 108
Views: 62,434
Posted By kentawan
V2 is superb! One of our run uses the same...

V2 is superb! One of our run uses the same library, once on the V1 and another on V2. The V1 run's cluster density was about 170(sorry i forgotten the exact unit, while V2 was 198.

Our V1 run gave...
Forum: Vendor Forum 03-30-2015, 03:45 PM
Replies: 108
Views: 62,434
Posted By kentawan
Hi guys, Just to take note that the v2...

Hi guys,

Just to take note that the v2 chemistry requires NCS 1.4

NCS 1.4 is NOT BACKWARD COMPATIBLE for v1 kits. Better to clear up your V1 kits before proceeding with NCS 1.4 upgrades....
Forum: Bioinformatics 02-09-2015, 06:43 PM
Replies: 649
Views: 169,195
Posted By kentawan
Hi All, I have gotten my final...

Hi All,

I have gotten my final methyl_extractor output files based on my bismark output files which have a mapping efficiency of 56.6% (is this normal?).

Right now I am stuck on the research...
Forum: Illumina/Solexa 01-27-2015, 06:14 PM
Replies: 10
Views: 4,905
Posted By kentawan
I called my local distributor. He mentioned that...

I called my local distributor. He mentioned that shipment starts February 2015!
Forum: Vendor Forum 01-27-2015, 06:13 PM
Replies: 108
Views: 62,434
Posted By kentawan
I just gave my local distributor a call. He said...

I just gave my local distributor a call. He said that this kit will be ready for shipment on February 2015. Pricing will be the same as the v1 kits!

Finally some hope for NextSeq 500 users!
Forum: Illumina/Solexa 01-27-2015, 05:17 PM
Replies: 10
Views: 4,905
Posted By kentawan
Hi folks! How's everything? Is it safe to convert...

Hi folks! How's everything? Is it safe to convert to NCS 1.3.0 now? We are kinda scared after reading TS's comment and still stuck to 1.20 now.

By the way, what are the library concentration that...
Forum: Bioinformatics 01-26-2015, 06:43 PM
Replies: 313
Views: 99,616
Posted By kentawan
Hi Simon or anyone else, Is it possible to...

Hi Simon or anyone else,

Is it possible to edit the chromosome names in SeqMonk? I started my project using genomes downloaded from Ensembl FTP. As I proceed I realized that I needed data from...
Forum: Bioinformatics 01-26-2015, 06:11 PM
Replies: 313
Views: 99,616
Posted By kentawan
Hi, How many probes you have in your report?

Hi,

How many probes you have in your report?
Forum: Bioinformatics 12-11-2014, 11:22 PM
Replies: 8
Views: 11,025
Posted By kentawan
Those may be interesting things like...

Those may be interesting things like miRNA/lncRNA. If you have the resources you should look into them as well.
Forum: Bioinformatics 11-24-2014, 09:06 PM
Replies: 313
Views: 99,616
Posted By kentawan
Hi Simon, I ran the RNAseq Quantification...

Hi Simon, I ran the RNAseq Quantification Pipeline with these descriptions. Log value is on. "Transcript features over mRNA. Quantitated with RNA-Seq pipeline quantitation counting reads over exons....
Forum: Bioinformatics 10-19-2014, 07:07 PM
Replies: 313
Views: 99,616
Posted By kentawan
Thank you very much Simon for the headstart...

Thank you very much Simon for the headstart guide. I made significant progress with my data analysis over the week.

Just one question though, what does the output value of the DNA bisulphite...
Forum: Bioinformatics 10-14-2014, 05:17 PM
Replies: 313
Views: 99,616
Posted By kentawan
Hi all, are there any options that forces SeqMonk...

Hi all, are there any options that forces SeqMonk to use multiple processor cores?

I was running a intensity difference filter over a methylation call datasets from bismark. I was comparing two...
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