A question about Next Generation Sequencer - 未名空间MITBBS历史存档

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A question about Next Generation Sequencer

A question about Next Generation Sequencer# Biology - 生物学

t*r2011-02-14 08:02

1 楼

时间：2012/04/12
地点：北京
人物：父母
人数：2
签证类型：B2
签证状态：1000
签经结果：水果
感谢板上的经验，对我父母材料的准备，以及面试的准备，都有很大的帮助。回馈本版
，贴出我父母的签
经。
签证过程很顺利，准备的材料都没有打开，就是人挺多，10：00场，到快一点才出来。
按照板上攻略，我准备了给签证官的信，和一份材料清单。
VO看了我的信，然后问了几个问题，就给过了。根据爸妈描述，过程很轻松，跟聊天一
样，大概问题如下：
去美国干什么？（看儿子）
儿子干什么（读书）
在哪里读书（xxx）
孩子回国过么（每年都回）
你们准备什么时候去（孩子放暑假时，六月份）
孩子在那边学习怎么样 (学习很好啊)
有没有发什么论文（。。。不知道。。。）
然后就撕条过了。。。

e*s2011-02-14 08:02

2 楼

需要装备一个小办公室，大家喜欢那个方案？
左上角斜的是门，下面的蓝方块是柱子。左下角是个小文件柜和打印机。墙上的蓝条是
whiteboard。

t*t2011-02-14 08:02

3 楼

http://dealnews.com/OCZ-Revo-Drive-80-GB-PCIe-x4-SSD-Card-for-250-after-rebate-free-shipping/398522.html

l*n2011-02-14 08:02

4 楼

http://blog.andrewray.me/reactjs-for-stupid-people/
The good:
1. You can always tell how your component will render by looking at one
source file.
2. Bundling Javascript and HTML into JSX makes components easily
understandable.
3. You can render React on the server.
The Bad:
1. You DO NOT GET any of the following:
An event system (other than vanilla DOM events)
Any AJAX capabilities whatsoever
Any form of a data layer
Promises
Any application framework at all
Any idea how implement the above
2. The documentation is not "accessible" nor "good."
3. React is large for how little you get, including how little cross browser
support.
4. Flux is a concept, not a library. Since there's no agreed on event
library, model layer, AJAX layer, or anything, there are many different "
Flux" implementations, and they all compete with each other.

L*e2011-02-14 08:02

5 楼

What is the difference between 'mate-paired' and 'paired-end' sequencing.
I am totally confused when read papers. Are they the same meaning but
different words?
Thanks.

a*22011-02-14 08:02

6 楼

恭喜

H*J2011-02-14 08:02

7 楼

没看懂，这是一个人用的，还是3个人？
我进办公室第一天，就把电脑的背面对着门，其他的无所谓了，又不是自己家

【在 e******s 的大作中提到】

: 需要装备一个小办公室，大家喜欢那个方案？
: 左上角斜的是门，下面的蓝方块是柱子。左下角是个小文件柜和打印机。墙上的蓝条是
: whiteboard。

l*n2011-02-14 08:02

8 楼

I can implement my own model layer and event system and totally forget about
Flux or Redux.

W*a2011-02-14 08:02

9 楼

You need to understand how Illumina seq works. Two ends of the
library molecule anneal to two oligos on the slide, forming
a bridge, and a PCR is performed in situ to amplify this molecule
into a cluster. The efficiency and consistence of cluster forming
is limited by the size of the insert, you can't have very long
product (>1kb)
classical pair-ends are generated directly from short inserts
usually less than 1kb, so no special library preparation method is
required.
For mate-paired, the two ends are usually far apart, 2-5kb, you
can't amplify such long sequences on Illumina chip directly. To
sequences these long inserts, you need to convert them into
short mate-paired libraries basically by removing the sequences in
between. Now the two far apart ends are joined and can be sequenced
by standard Illumina or SOLID chemistry

sequencing.

【在 L******e 的大作中提到】

: What is the difference between 'mate-paired' and 'paired-end' sequencing.
: I am totally confused when read papers. Are they the same meaning but
: different words?
: Thanks.

z*f2011-02-14 08:02

10 楼

恭喜

b*u2011-02-14 08:02

11 楼

没有谁希望电脑被人看见吧，都设计成电脑屏幕对墙比较好吧。

【在 e******s 的大作中提到】

: 需要装备一个小办公室，大家喜欢那个方案？
: 左上角斜的是门，下面的蓝方块是柱子。左下角是个小文件柜和打印机。墙上的蓝条是
: whiteboard。

l*n2011-02-14 08:02

12 楼

The good thing about React is that I can use it on the server side. I found
that is convenient and awesome.

L*e2011-02-14 08:02

13 楼

I am going to use SOLiD system.
There is two libraries i am going to prepare:
1), Regular fragmentation, 150 bp / fragment, then link to adaptors.
2), Mate-paired: link two ends of a fragment (1-2 kb) together. (i had
thought that is why also called 'paired-end') .
According to your description, pair-ends is the regular fragments, but why
was call 'pair-ends', is that because it was sequenced from two ends?
Thanks

c*n2011-02-14 08:02

14 楼

xmjdh!

m*t2011-02-14 08:02

15 楼

其实最重要的就是有哪些人可以看到别人的screen, 而哪些人的screen是别人看不到的。
其他的都是其次。

【在 e******s 的大作中提到】

: 需要装备一个小办公室，大家喜欢那个方案？
: 左上角斜的是门，下面的蓝方块是柱子。左下角是个小文件柜和打印机。墙上的蓝条是
: whiteboard。

w*s2011-02-14 08:02

16 楼

取代node.js ?

found

【在 l**********n 的大作中提到】

: The good thing about React is that I can use it on the server side. I found
: that is convenient and awesome.

W*a2011-02-14 08:02

17 楼

yes, because when Illumina first developed the seq platform, the
default is to sequence from just one end of the molecule with one
primer. They soon came up with the pair end module, allowing two
seq rxns to be performed sequentially and get sequences from both ends.
PE is backward compatible with single end seq, so nowadays most kits use
PE primers, and you have the option to sequence just one end of it.
I think mate-paired gets its name because you 'mated' the two
ends together, so in the end product they are next to each instead.
Pair-end, from what I understand, means the two reads come from the
ends of the same molecules, so they are 'pairs'. It is just a trivial
terminology thing.

had
but why

【在 L******e 的大作中提到】

: I am going to use SOLiD system.
: There is two libraries i am going to prepare:
: 1), Regular fragmentation, 150 bp / fragment, then link to adaptors.
: 2), Mate-paired: link two ends of a fragment (1-2 kb) together. (i had
: thought that is why also called 'paired-end') .
: According to your description, pair-ends is the regular fragments, but why
: was call 'pair-ends', is that because it was sequenced from two ends?
: Thanks

S*22011-02-14 08:02

18 楼

恭喜

l*t2011-02-14 08:02

19 楼

你是老板的话就6，不是就3

【在 e******s 的大作中提到】

: 需要装备一个小办公室，大家喜欢那个方案？
: 左上角斜的是门，下面的蓝方块是柱子。左下角是个小文件柜和打印机。墙上的蓝条是
: whiteboard。

m*T2011-02-14 08:02

20 楼

基本的理解是正确的。
1)pair-end(PE)用的是regular frag lib，但是两头读（分别称为F3和F5），但读的还
是同一片段；
2)mate-pair(MP）则是因为在lib construction过程中用了circulization而且有
internal adaptor(IA)，所以是两个片段(分别称为F3和R3)中间被IA分隔开，实际上读
取的是两个片段。
画个简单的示意图：
PE: ACGTTTCGA........GTACCTA
F3-> MP: ACGTTTCGA........GTACCTA-Internal adapter-ATCGGCTA.......
F3-> R3->

why

【在 L******e 的大作中提到】

c*72011-02-14 08:02

21 楼

恭喜

p*r2011-02-14 08:02

22 楼

我个人喜欢3，比较一起沟通。
btw，我是自己一个人办公室，
之前屏幕背对门口，
现在改成一排屏幕正对门口，路过的人都可以看到我在干嘛。
一个是光明正大，做个其他小弟看样子，
另一个也是对自己的一个督促，
免得自己一不留神就去灌水，看新闻了。

L*e2011-02-14 08:02

23 楼

Many thanks to you two . It is quite clear for me now.

B*L2011-02-14 08:02

24 楼

恭喜

y*c2011-02-14 08:02

25 楼

楼主你这图是怎么做的

e*e2011-02-14 08:02

26 楼

很清楚.这个应该马一个了吧.

【在 m***T 的大作中提到】

: 基本的理解是正确的。
: 1)pair-end(PE)用的是regular frag lib，但是两头读（分别称为F3和F5），但读的还
: 是同一片段；
: 2)mate-pair(MP）则是因为在lib construction过程中用了circulization而且有
: internal adaptor(IA)，所以是两个片段(分别称为F3和R3)中间被IA分隔开，实际上读
: 取的是两个片段。
: 画个简单的示意图：
: PE: ACGTTTCGA........GTACCTA
: F3-> : MP: ACGTTTCGA........GTACCTA-Internal adapter-ATCGGCTA.......