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Forum: Illumina/Solexa 03-28-2017, 10:35 PM
Replies: 1
Views: 548
Posted By mkdir
Question bacterial wgs library loading on MiSeq v3 600 cycles

Just wondering how much wgs library (prepared by Nextera xt kit) should be loaded on MiSeq using v3 600 cycle kit. We tried two times, 20 pM and 14 pM, both runs yielded only ~7 gb (half of 15 gb)....
Forum: Oxford Nanopore 11-03-2016, 12:31 PM
Replies: 32
Views: 13,616
Posted By mkdir
Smile Hi gringer, thank you very much!

Hi gringer, thank you very much!
Forum: Oxford Nanopore 11-03-2016, 11:49 AM
Replies: 32
Views: 13,616
Posted By mkdir
Hi gringer, thank you very much for the...

Hi gringer, thank you very much for the information. The nanopore website suggested 21Gb (Product specifications comparison, https://nanoporetech.com/products#comparison). But you have answered all...
Forum: Oxford Nanopore 11-03-2016, 11:19 AM
Replies: 32
Views: 13,616
Posted By mkdir
This 48 hr run generated ~ 300 Mb data, is this a...

This 48 hr run generated ~ 300 Mb data, is this a usual case?

We tested a 2 hr run, and only generated 29 Mb data. But the protocol said 48 hr should generate 20 Gb. Are there any tricks to...
Forum: Oxford Nanopore 10-27-2016, 08:49 PM
Replies: 4
Views: 1,798
Posted By mkdir
Hi wdecoster, thank you very much for the...

Hi wdecoster, thank you very much for the suggestions. We didn't quantify the samples after shearing by nanodrop or other quantification kit. But we tested the sizes of the sheared lambda DNA with...
Forum: Oxford Nanopore 10-27-2016, 08:29 PM
Replies: 4
Views: 1,798
Posted By mkdir
Ola, Thank you very much for the information.

Ola, Thank you very much for the information.
Forum: Oxford Nanopore 10-26-2016, 09:03 PM
Replies: 4
Views: 1,798
Posted By mkdir
Lambda control library problem

We have had happy experience with 454, pgm and illumina libraries. However, when we followed the minION Lambda DNA control library protocol, we can only get 25 ng DNA instead of the expected 250 ng. ...
Forum: Oxford Nanopore 09-26-2016, 09:31 PM
Replies: 2
Views: 1,271
Posted By mkdir
Red face library with different sizes

I wish to use MinION to sequence 11 PCR products. Most of them are ~ 2 or 3 kb. Another two are 4kb and 9kb respectively. Is it possible to add the adapter and run them together, although they have...
Forum: Oxford Nanopore 07-28-2016, 08:52 AM
Replies: 5
Views: 1,749
Posted By mkdir
Hi GenoMax, thank you very much for reminding.

Hi GenoMax, thank you very much for reminding.
Forum: Oxford Nanopore 07-28-2016, 08:47 AM
Replies: 5
Views: 1,749
Posted By mkdir
Hi Markiyan, Thank you very much for explaining...

Hi Markiyan, Thank you very much for explaining the details. These help a lot.
Forum: Oxford Nanopore 07-27-2016, 11:10 PM
Replies: 5
Views: 1,749
Posted By mkdir
Question Questions

Hello,

I am a newbie to Oxford Nanopore sequencing technique. I have a couple of questions. How many active nanopores will be good enough? Is the account activation of metrichor required to run...
Forum: Bioinformatics 07-02-2013, 12:00 PM
Replies: 0
Views: 602
Posted By mkdir
which software can draw protein locations on scaffolds/chromosomes

Hello, I am wondering which software can draw protein locations on scaffolds/chromosomes, and can draw ortholog connection (use lines to connect) between two scaffolds/chromosomes (I have ortholog...
Forum: Bioinformatics 12-11-2012, 02:20 PM
Replies: 2
Views: 625
Posted By mkdir
MEGAN worked well. Thank you very much, jimmybee

MEGAN worked well. Thank you very much, jimmybee
Forum: Bioinformatics 12-10-2012, 03:29 PM
Replies: 2
Views: 625
Posted By mkdir
how to get kingdom counts from a list of species

Hello,

I need to look at the contamination percentage of some genome sequencing data. I got a list of species from blastn hits. I am wondering whether there are some softwares can group the...
Forum: Bioinformatics 11-02-2012, 02:45 PM
Replies: 15
Views: 5,977
Posted By mkdir
I got the same problem, cannot figure out......

I got the same problem, cannot figure out......
Forum: Bioinformatics 10-30-2012, 01:02 PM
Replies: 4
Views: 7,306
Posted By mkdir
Thank you very much kmcarr and maubp. This worked...

Thank you very much kmcarr and maubp. This worked out.
Forum: Bioinformatics 10-29-2012, 12:29 PM
Replies: 4
Views: 7,306
Posted By mkdir
protein gi number to description

Hello,

I got gi numbers for blastp -outfmt 6 results. I am wondering which programs and database can convert the gi number list to protein descriptions. Any help? Thank you very much.
Forum: Core Facilities 05-13-2012, 07:26 PM
Replies: 3
Views: 1,951
Posted By mkdir
Hi Wallysb01 and scbaker, thank you very much for...

Hi Wallysb01 and scbaker, thank you very much for your helpful information.
Forum: Core Facilities 05-12-2012, 01:53 PM
Replies: 3
Views: 1,951
Posted By mkdir
Looking for a good illumina core facility

Hello, I am new to illumina sequencing. I am wondering how many total bases I can get if I spend ~ $3000 for PE 100 bp, one lane. And how many bases can be used after quality filtering. Are there any...
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