n****2
发帖数: 307 | 1 FYI:
http://www.amazon.com/Seiki-SE50UY04-50-Inch-120Hz-HDTV/dp/B00B
Ok. I got this in the mail today and wasn't sure if it would work with my hp
dv7 laptop with an intel hd3000 graphics card (HDMI only out). When I first
opened and connected to this monitor the resolution defaulted to a maximum
of 1920x1080 @ 24 Hz. It was pretty sharp but the last TV I had was just as
sharp at that resolution.
So I spent all day working with different modelines to try to manually get
the resolutin right. The m... 阅读全帖 |
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l**********1
发帖数: 5204 | 2 Continue:
3)
//www.mdpi.com/1099-4300/11/4/606/
4)
//digitalcommons.unl.edu/chemeng_news/12/
5)
//vixra.org/pdf/0910.0067v3.pdf
6)
//www.bio.unipd.it/bam/PDF/7-3&4/art15.pdf
7)
//chfpn.pl/files/?id_plik=401
8) Google Book:
//books.google.se/books?id=PbS_moKY-nYC&pg=PA125&lpg=PA125&dq=negatives+
entropy+++uphill++Chemical+Thermodynamics++Prigogine&source=bl&ots=
KUcdUIQDBO&sig=Ly3zqw7ULTtReO4l6YUUmwD_IWM&hl=sv&sa=X&ei=QCx4T_
H5EpPE4gSxo5SFDw&sqi=2&ved=0CHgQ6AEwCQ#v=onepage&q=negatives%20entropy%2... 阅读全帖 |
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p******n
发帖数: 874 | 3 100M per run, the through put is too low. Now to sequence a human genome
that have enough coverage (30x), the bam file has a size of 100G. |
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o********r
发帖数: 775 | 4 你这个太杯具，还是赶快找一个已经建起pipeline的组合作，要自己做的话2个月都来
不及摸条件的。别以为软件可以直接用就很方便，不同的软件间可能根本不能直接对接
，比如BAM中用不用chr，排序的时候是1,10,11,...,2，20,21,22,3，...,9,X,Y还是1,2,..
.,9,10,11,...,22,X,Y（这几种居然都是常用的）都可能造成程序崩溃，更别提有些莫
名其妙的软件还有特殊的输入格式。。。另外每个软件都有一推各种各样的参数，不合
适的参数结果就是垃圾 |
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A*****n
发帖数: 243 | 6 -u + 管道还是能省不少IO上的时间的。楼主总共也才200M reads。最后得到的BAM应该
也就在２，３０G这个数量级，不会有特别大的麻烦。
顺便问一下，哪些软件这么bt，下次遇到的时候好注意一下。 |
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o********r
发帖数: 775 | 7 给你个我遇到过的变态软件：cnver，这家伙用的BAM居然不是coordinates sorted。至
于chr以及排序不同的就太多了，俺遇到过的软件两种格式基本是一半一半 |
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s****p
发帖数: 1087 | 8 看此人的简历：
Research Computer Scientist ->
Senior Research Computer Scientist ->
Senior Research Scientist ->
Associate Research Professor
http://www.cs.cmu.edu/~bam/resume.html
Human Computer Interaction Institute
Professor, 2004 - present.
Associate Research Professor, 2003 - 2004.
Senior Research Scientist, 1995 - 2003.
Computer Science Department
Senior Research Computer Scientist, 1992 - 1995.
Research Computer Scientist, July 1987- 1992.
School of Computer Science, Carnegie Mellon University... 阅读全帖 |
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G***G
发帖数: 16778 | 9 given a NGS data (bam files), how to determine its species? |
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j*p
发帖数: 411 | 10 How did you get this bam file? |
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G***G
发帖数: 16778 | 11 given a NGS data (bam files), how to determine its species? |
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j*p
发帖数: 411 | 12 How did you get this bam file? |
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l**********1
发帖数: 5204 | 14 For your FAQ:
a)
外界的负熵除了阳光主要来自于哪里？
RE:
white hole
please go to
//vixra.org/pdf/0910.0067v3.pdf
b)
疾病的熵增加以及药物增加负熵流如何通过实验测量？负熵流是否有此可以成为
RE:
Exactly i do not know detail about your ask which belongs to a micro aspect
but for macro aspect please go to:
//www.bio.unipd.it/bam/PDF/7-3&4/art15.pdf
or
//digitalcommons.unl.edu/chemeng_news/12/
c) : 怎样检测药物使系统达到或者接近临界点，有没有可能通过药物改变临界点本身？
RE:
Exactly i do not know detail about your ask which belongs to a micro aspect
but for macro aspect please go to:
//chfp... 阅读全帖 |
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c*****g
发帖数: 66 | 15 add this option when you view the bam file
-f 0x10
check with sam spec to make sure the flag is right. |
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w****w
发帖数: 521 | 17 新的sra toolkit里已经有一个sam-dump工具,跑10G以下的小文件没什么问题，100G以
上的，跑一个2，3个礼拜还可以接受。同时跑两个，performance马上不行，要20，30
个礼拜才能完成。 |
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w****w
发帖数: 521 | 18 傻了，sam-dump可以直接extract。我们感兴趣的只有几个小region,抓出来很快。不幸
的是好几个大文件都出错了。 |
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j*p
发帖数: 411 | 19 still did not get LZ's point. but whatever. |
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w****w
发帖数: 521 | 20 我拿到的文件应该都是cSRA,虽然都是sra extension. |
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c*****g
发帖数: 66 | 21 这个事情很简单：
1. 根据A做一个bed file
例如
chr1 1239 1240
注意，bed是0起始的
2. samtools mpileup -l snpA.bed your.bam
and pipe the output to whatever you want.
directly reading line by line from a SAM (like you described) is a bad idea.
略） |
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i***r
发帖数: 1035 | 22 我手上的bam 文件似乎排序有点问题（我转成sam之后，第一列是这样）：
chr1
chr10
chr11
...
chr2
chr21
...
chr3
会不会有问题？
idea. |
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u*********1
发帖数: 2518 | 23 你要确定你BWA产生bam file时候使用的ref，和你GATK command里的ref，是同一个
reference；GATK对这个要求很严，尤其不同版本的ref，比如g1k_37和hg19；g1k会包
含一些无法assembly的contig。总之ref里的chromosome的多少，排序都很重要，同时
要注意prefix比如“chr”；20和chr20是不一样的，GATK没办法识别的 |
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u*********1
发帖数: 2518 | 24 作为一个曾经0基础的菜鸟，我还是蛮有体会的。
想想一年前我连linux里的grep都不晓得是啥。老板说“grep”，我说gre。。啥？greb
吗？老板摇摇头说you really have a lot to learn...不过老板超好，想办法给我把
各种基础的东西讲清楚。。。包括RAM是啥。。汗。。。
做NGS/bioinformatics的，我觉得核心思想还是：如何利用计算机手段解决生物问题。
说起来简单但未必每个人都深刻体会的到。什么python/bash/perl啥啥的，要入门很快
，但也绝对不是什么两个星期就搞定。我现在和python打交道也一年了，但也完全就是
个皮毛，主要是你自己的project决定的。。如果你永远只需要简单的process下你的
text，而且text如果不大比如100MB，你可以永远for line in text。。或者readlines
（），但如果碰到很大的text，就不能readlines（）了因为cluster可能没有那么大的
memory to load the whole text.
所以我觉得就是现学现用，除非你是CS系科班搞计算出身... 阅读全帖 |
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u*********1
发帖数: 2518 | 25 samtools view -F 4 map.bam
4 (in decimal) or 0x0004 (in HEX) indicates that the query read is unmapped.
If you use the filter option (-F 4) you will remove unmapped reads, hence
the output will only contain mapped reads.
This flag will extract any mapped reads regardless of what mate pair looks
like.
If you'd like to account mate pair, please look at the link below:
http://www.biostars.org/p/14518/ |
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i******w
发帖数: 407 | 26 比如 GGATCC 变成了 GGAACC，Bam HI 还能cut吗？效率会降低多少呢？谢谢 |
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Z******5
发帖数: 435 | 27 标准Bam H1 buffer下，完全切不动了吧，没有什么效率降低不降低这一说。 |
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P****d
发帖数: 564 | 29 不知道有没有什么quantum dots之类的东西，每电一下，就改变一次状态。最后拿出来
读一下。
人脑本身又是个大问题，不能做完实验直接捣碎。
I once heard from one of the mater minds behind the human genome project,
who I have a lot of respect for (not Lander, he's more of a showman than
scientist to me), that we tend to be over optimistic on short term goals but
over pessimistic on the long term ones. So I do have a lot of hopes for
BAM -- not in the grandiose goal itself, but I think it will drive a lot of
technology development in the process that will change... 阅读全帖 |
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b******k
发帖数: 2321 | 30 非常赞成 BAM唯一让我觉得还值得乐观的就是tool development了，也许在长期看会对
neuroscience有很大贡献。至于数据本身，我觉得会和ENCODE这种project一样基本啥
用都没有
but
of |
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s******9
发帖数: 283 | 31 Alivisatos AP, Andrews A, Boyden E, Chun M, Church G, Deisseroth K, Donoghue
J, Fraser S, Lippincott-Schwartz J, Looger L, Masmanidis S, McEuen, P,
Nurmikko, A, Park H, Peterka D, Reid C, Roukes M, Scherer A, Schnitzer M,
Shepard K, Tsao D, Turrigiano G, Weiss P, Xu C, Yuste R, Zhuang X (2013)
Nanotools for Neuroscience and Brain Activity Mapping. ACS Nano. in press |
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d*****r
发帖数: 2583 | 33 I think whoever being able to join this club is too high now.
It's all about money, big money. |
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o*****r
发帖数: 39 | 35 She has worked on neuron for a while. |
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F*Q
发帖数: 3259 | 36 That is it! Everything is about money. Who really cares about science? |
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w***x
发帖数: 265 | 38 所有的omics里，economics是最管用的
——sydney brenner |
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a********k
发帖数: 2273 | 40 Speaking in the crackling cadence of his native South Africa, Brenner took
delight in piercing the latest biological trends, including the
proliferation of “omic sciences.”
“I was asked by a business journal in England, The Economist, which was the
most important omic science for biotechnology, and I gave them the obvious
answer: it was that science called econ-omics,” he chuckled. |
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o*****a
发帖数: 2335 | 41 这老爷子有喜剧天才，走到哪演到哪
the
obvious |
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f**********e
发帖数: 1994 | 42 此公来 UCSF 演讲时，用了零张投影片，零个 powerpoint，一步没离开讲台，一个手
势没用，照样很有娱乐效果。
演讲主题：systems biology 是屎。 |
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w***x
发帖数: 265 | 45 提到brenner，就想起这群人里之一的yuste早年的故事
当年小yuste在西班牙学医，快毕业的时候慕名跑到LMB跟着brenner做了一年研究，本
来想留在LMB,不料老爷子告诉他英国已经没落了，快点去米国吧！
于是yuste飘扬过海，去了洛克菲勒，做了wiesel和katz的学生。。。
Donoghue |
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b******k
发帖数: 2321 | 47 我其实非常不理解现在推brain actiivty map的根基何在，在我看来这就是个从概念（
为什么觉得activity map重要？为什么不是connetivity map，不是chemical map决定
了大脑功能？），到技术（几篇review里提到的新技术idea与其说是技术，不如说是科
幻）都远不成熟的想法，为什么现在就急吼吼的上大项目去搞？
类比一下HGP，当时骂的人也不少，但是HGP之前至少用sager seq测一个物种的序列已
经很成熟了，无非是human genome大一点而已。
另外再补充一点，炒connetome也好，炒BAM也好，这些人上来就是human brain或者至
少mammalian brain。就这一点上我就觉得与其说他们想做science，还不如说他们想圈
钱。否则的话完全可以从最简单的动物做起，来个优美的proof-of-concept再说。线虫
的connetome早就有了，从中我们得到什么信息编码的algorithm了么？没有，还是得靠
wet lab一点点描述。cortex上几百个neuron级别的activity map也有不少了吧，我... 阅读全帖 |
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l**********1
发帖数: 5204 | 48 Pls check,
i) Trapnell C et al., (2012).
Differential gene and transcript expression analysis of RNA-seq experiments
with TopHat and Cufflinks.
Nat Protoc 7: 562–578.
ii) Li H et al., (2009).
The sequence alignment/Map format and SAMtools.
Bioinformatics 25: 2078–2079.
plus
Weikard R et al., (2013).
Identification of novel transcripts and noncoding RNAs in bovine skin by
deep next generation sequencing.
BMC Genomics. 14: 789. [Epub ahead of print]
>http://www.ncbi.nlm.nih.gov/pubmed/24225384
c... 阅读全帖 |
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