a***e
发帖数: 1010 | 1 your sample --> company --> FQ or FA file
--> blat or bowtie or Tophat to align --> (.sam, .bam file)
--> Samtools or GATK to call variants --> .vcf file (excel file)
--> igvtools or genome browser to visualize
or it is said u can use CLC to replace the last three steps. |
|
v***r
发帖数: 1046 | 2 就是说公司给的是aligned好的bam文件，接下来不就是用samtools, GATK做snp
calling吗？为什么不是很容易搞定呢？难点在哪? |
|
k****z
发帖数: 1863 | 3 you have bam files ?
then use IGV |
|
w****w
发帖数: 521 | 4 仪器自带的软件可以输出fastq,连bam都可以帮你产生。 |
|
C*********s
发帖数: 31 | 5 才知道cell line原来这么翻译的。。。
cbioportal很不错 TCGA的分析结果基本都在了 来源应该是Broad 只是不支持大规模的
数据下载 可以自己写写script去query 用不着cs master
TCGA的原始数据 如果是bam file 是需要账号的 我记得只有美国的pi才行 也用不着cs
master
从cghub下载 https://cghub.ucsc.edu/docs/user/download.html |
|
s******s
发帖数: 13035 | 6 我说了， NGS的BAM和FASTQ都在CGHub； 所有其他能infer sequence的东西，比如
genotype, vcf，要password；其他的一切东西，包括蛋白分析，methylation, cnv,
maf(tumor - normal)， gene表达， 等绝大多数，都在open access, 基本上都能
assembler弄下来。
你的450k，估计你不会自己去分析raw data吧，分析过的beta value啥都很小的。
用assembler搞450k尤其方便，因为它可以帮你搞gene level的平均，然后把gene
名字搞成hugo. TCGA的gene model是GAF2，那个是用起来相当的头痛，和其他地方
数据比较的烦死我。
matrix |
|
s*****5
发帖数: 52 | 7 同问。请问各位行家，umanpped.bam文件能直接用trinity做分析吗？trinity是不是必
须linux环境运行？谢谢。 |
|
x*****d
发帖数: 704 | 8
你得先用bam2fastq之类的软件把bam转成fastq，然后才能导入trinity。 |
|
r**********e
发帖数: 587 | 9 说下我的comments吧
DELLY其实是比较新的软件，综合了paired-end discordant和split-read两种signal来
make calls，自然是不错的，而且也是1000genome使用的软件之一，而且最后结果提供
vcf format
SV领域最早最原始的三个软件，我个人认为的，read-depth的CNVnator；discordant的
breakdancer；以及split-read的Pindel；后续陆陆续续出来了很多类似软件，其实大
同小异，很多都是为了发文章而发文章的trash paper。上面说的三个软件，虽然都是
基于一种signal，但都算元老，1000genome使用的软件，而且关键是有四五年历史，很
多人使用，所以一直在update，debug，maintain，使用起来比较上手。但CNVnator是
不可能计算translocation的，Pindel可以找到translocation但Pindel是针对比较小的
structural variation，因为big SV的computational cost太高
还有一个超级好的... 阅读全帖 |
|
m******c
发帖数: 830 | 10 Sounds interesting. Do you offer bam file, other than GATK best practice? |
|
b********w
发帖数: 334 | 11 Beta 期间，你要求bam文件，我们会提供的。版上已经至少有三位得到原始数据了。 |
|
b********w
发帖数: 334 | 12 直接面向个人
Tech Details:
- FDA approved Saliva collection kit.
- Agilent SureSelect V5 50MB chip
- 75x on target coverage (after mapping, filtering, and duplicate removal,
130-140x raw throughput)
- 99% Coverage > 1x
- 90% Coverage > 20x
- CLIA certified Illumina sequencing.
Deliverable
- Ownership of your genome
- VCF file (Beta 期间你要原始数据 BAM，我们也可以提供。)
- CLINVAR, CGD summary about your variants
- Traits
- Beta 期间你要原始数据，我们也可以提供。
Public exposure
Genomeweb:
https://www.genomeweb.com/molecular-diagnost... 阅读全帖 |
|
m******c
发帖数: 830 | 13 Sounds interesting. Do you offer bam file, other than GATK best practice? |
|
b********w
发帖数: 334 | 14 Beta 期间，你要求bam文件，我们会提供的。版上已经至少有三位得到原始数据了。 |
|
t**x
发帖数: 20965 | 15 BAM文件应该对beta用户继续提供吧。
刚刚请求了数据, 信发到support了。请楼主能不能回答我的邮件？ |
|
b********w
发帖数: 334 | 16 Bam会继续给beta user提供。
9月7号，已经回您的request了。没有下载吗？
还是其他账户？ |
|
b********w
发帖数: 334 | 17 try Genos 吧
我们给原始数据，现在beta中，bam, fastq你要也会给。 |
|
b********w
发帖数: 334 | 18 对一般消费者
1. 我们会提供一个界面去浏览你的variant信息，我们会报告你的exome里面和CLINVAR
数据库匹配的结果，一般大致有1000-1500 个位点， 按照pathogenic, likely
pathogenic, VUS, likely benign, 和benign分类。忠实反映CLINVAR的结果没有多余
的解读。关联相关文献。同时按照CGD疾病把variant分类。再有就是一些
entertainment的traits
2. Genos给VCF文件，VCF包括所有位点的信息，不仅仅是界面展示的位点。你自己下载
了VCF文件，你有自由去其他的解读服务。未来Genos会引入第三方提供深度解读的
partner. （目前有在谈，10刀左右吧）
3. 不排除以后我们给报告。
如果你是bioinformatician, 我强烈推荐Genos
现在是beta, Genos可以提供更原始的数据 比如，bam文件。分析自己的数据比分析别
人的数据好玩多了。
可以私信一下email， 我给你发内测VIP invitation. |
|
s******s
发帖数: 13035 | 19 这个东西的主要问题是储存，分析不难，现有的分析流程有很大的优化，或者
GPU/专门芯片加速的潜力。
在我看来，如果测序成本降低到一定数量级，那么是否保存原始数据就值得讨论了。
要么有其它的高压缩格式，不必要capture所有的BAM信息；要么直接保存variant。 |
|
c******o
发帖数: 1184 | 20 连bam都要省掉？
variant calling 选项那么多，光package就好几个，而且还要根据平台和coverage微
调，这样没法重复阿，过几年你人一走或者package一更新，后面的人就傻眼了 |
|
s******s
发帖数: 13035 | 21 偶像啊。
估计是不愿意烦心申请funding，比较enjoy干活，一旦做PI一般80%的时间就废掉了
吧。
Heng Li的影响还是远远超过一个BWA的，虽然这个就已经很夸张了。要知道GRCh38
很多序列也不过是Heng Li在N年前做的37的decoy序列。要知道SAM/BAM以及VCF这
种二代分析的标准格式都是那个小团队的（最近刚送给GA4GH). 可以这么说，他基本
上就是二代测序的幕后黑手了，就这两个标准格式，就极大的加速了几乎所有的NGS
应用开发
PI？ |
|
发帖数: 1 | 22 GoooG：sam，bam和samtools是一起做的。没有先后。一直都是公开的。
cellcreator：可以试试stampy，毕竟它是少数考虑了高突变率的short-read mapper。
但不知效果会怎样，没有经验。你也可以考虑先组装再比对。高heterozygosity可能同
样难办，不过有时间的话可以试一个样品。
dimorphism：我很欣赏跟生物密切结合的应用，所以Erez Lieberman更牛。
profile：谢谢你的鼓励和你前面的祝福，谢谢！ |
|
f********r
发帖数: 30 | 23 cram 只能压缩SAM/BAM吧？他们这回的目标是fastq。做压缩MPEG那边是在行的。缺的
应该是第一线分析数据的人。不过现在有UK Sanger的人在一起做。 |
|
发帖数: 1 | 24 做一回雷锋
如果你想从raw fastq data到结果，大概两个步骤：
1. raw fastq--bwa--mutation/gene expression
主要是read mapping，把GB level的原始数据BWA mapping得到bam file，然后如果你
的目标是找variants那就用GATK这样的主流软件
1a. 对于你来说，这个步骤里你主要需要学会linux environment，bash，学会用HPCC
来submit job，学会tune BWA/GATK的参数，是很容易的。
1b. 同时你要学会面对big data，都是比如300 million行的数据，处理一个全基因组
需要1TB空间，这个是很可怕的。大数据的storage，transfer都要注意。
1c. 什么BWA/GATK这种复杂算法高级原理C/JAVA的你不需要care
你可以理解这一步就是从海量海量的数据里初步filter出你要的东西，但是粗糙的东西
，不是完整产品
2. gene expression---统计分析/美丽的图图
这个主要是RNA-seq，你tophat之类的得到一堆基... 阅读全帖 |
|
l*******e
发帖数: 1485 | 25 学物理的做什么的都有，关键是要看具体经历。
本科物理到美国直接读电路PhD几乎门儿都没有。
读电路硕士就另当别论了---花钱上学的事儿。先自费电路硕士，然后再申请电路博士
是完全可能的。
好上手路子又宽的，CS。
【 bams (初来匝道，请多关照～～),
也看各人能力了.
你说的这两个，可能学物理的比较好上手，但是路子太窄了。
我认识不少几个以前学物理的，现在做circuit design。还有，如果数学比较好的话，
可以考虑signal processing。 |
|
g*******a
发帖数: 1383 | 26 i'll search around
i was wondering if a scanner can do this, why not w/ some kind of
special camera, taking a pic of some surface and bam! you got the
point-cloud on the computer |
|
w*********l
发帖数: 5144 | 27 多去参加local会议, 有bams, CACO和别的. |
|
s**a
发帖数: 8648 | 28 政治局是核心，但是核心里面还有胡核心呀。就那么几个人，就都变成informal的东西
了，都是informal negotiation，threat，guesswork了吧。这件事情，美国的大报都
登了。
下面是victor shih blog上面的评论，
So, here I was, going about my boring life, and BAM, we find out that
Shanghai Party Secretary Chen Liangyu has been dismissed. This time, there
would be no face-saving "illness" or "promotion" to the CPPCC. Like Chen
Xitong before him, the Hu-Wen leadership is using Chen as a way to send a
credible signal to all of the local officials about who is in charge. Chen
will |
|
a****1
发帖数: 160 | 29 BAM is very good, but the pay for risk people is not as good as investment
people. |
|
a****1
发帖数: 160 | 30 BAM is very good, but the pay for risk people is not as good as investment
people. |
|
r**********d
发帖数: 510 | 31 Is bam still hiring?
fund |
|
m*********k
发帖数: 10521 | 32 [Donation] tin Nov 6 ● 热烈庆祝OCEF和OSCCF夺得总冠军和季军
10*603=6030
扣除版面:(Donation)6030伪币成功
成功奖励 10 伪币的用户: a9254678, absmit, acetone316, Achu, ADME, ADOMET, ADSP, advisor, Against, AirJordan, akju, aladdin, alicelast, alive, allein, allthesame, amethystor, AmFarmer, amy2009, andreth, angelflaree, aniee, anonymaus, aoyiwumi, apple51, applebigbig, AprilFlower, aprilmom, aragorn, Ardone, ariescb, armslave, arnao, asdl, astro, asus, Auction, AUV, avon810808, Awen, ayoung17, badcompany, bam |
|
|
z*******n
发帖数: 1034 | 34 Did you know that Android has a built-in mechanism for locating or locking
your lost phone? Google hasn’t done the best job marketing it, but it’s
actually been baked right in since the release of Android 4.4*.
(It works with older Android phones, too — you just have to install the
free app yourself)
Today that feature gets even better, thanks to the addition of a trick that
seems so obviously great in hindsight: your lost phone can be set to call
you — and only you — as soon as someone finds it... 阅读全帖 |
|
R*******e
发帖数: 25533 | 35 Mark Knopfler - Boom, Like That
http://www.youtube.com/watch?v=dvj4svKcjl0
I'm going to San bernardino ring-a-ding-ding
Milkshake mixers that's my thing, now
These guys bought a heap of my stuff
And I gotta see a good thing sure enough, now
Or my name's not kroc that's kroc with a 'k'
Like 'crocodile' but not spelled that way, yeah
It's dog eat dog rat eat rat
Kroc-style boom, like that
The folks line up all down the street
And I'm seeing this girl devour her meat, now
And then I get it, wham as... 阅读全帖 |
|
l****r
发帖数: 21884 | 36 管子上面的, 只说官方mv.
论点击率小有其中的一个版本有5万多, 小孤单1万2, 小冬天接近8千, 考虑到时间因素
, 小冬天未来超过小孤单应该是肯定的.
三个对比, 发现我最满意的是小孤单的mv, 胜在与歌曲融合的好,男主在里面非常帅而且
玩得很开心的样子. 小有里面陈里很帅可是mv拍得实在不知所云, 小冬天倒是有内容可
是陈里那个时候他可以说是身心交瘁, mv里面掩饰不住的憔悴也是情有可原了.
小孤单的mv评论中还有一个孤单粉, 呵呵.
"I can't believe I like his song this much.
I never got how he was such a big deal, wasn't imrpessed with You mei you
gao shu ni and then, bam! Now I'm freaking in love with this song."
和大家一起复习一下帅酷有型的孤单里
http://www.youtube.com/watch?v=8LCoASVrjF4 |
|
z**l
发帖数: 1192 | 37 哦... 偶没秤. 估计 7lb 左右.
一个30ft抛钓(over a kelp bed), 线刚收紧, BAM! 80lb braid 都有些失控, 感到鱼
在水下巨大的摇动. 偶接连紧线, 竿高举, 弯90度... PENG, PENG, PENG...PENG,
PENG, PENG... PENG, PENG, PENG...好爽!
最后鱼卡在15ft远的Kelp里,是还看不到头, Cabezon? Lingcod? 感紧呼唤队友划过去.
没有抄网, 仗着竿硬线粗, 拖出Kelp入船, Big Fat Grass.
秘密武器等包子, 嘿嘿嘿. |
|
V**C
发帖数: 239 | 38 来自主题: _Auto_Fans版 - 疯了。。。 no no, u should leave it to him...
he needs to show up in his convertable wearing the jacket pimping like a
rock star...bam, girls dig tat..lol... |
|
w*******y
发帖数: 60932 | 39 Via facebook deals Chipotle will be giving BOGO burritos on11/13-14 and 11/
20-21. All you need to do is use facebook mobile and use places to find
deals. Show employee your phone and bam BOGO! They have a few other deals
available immediately but none as good as this
|
|
w*******y
发帖数: 60932 | 40 Saw the Zipcar folks at the mall showing off the new Prius Plug-In Hybrid.
They were handing out flyers--I'm not sure what the code is for new signups,
but for existing members:
Go to Link:
http://zipcar.com/gift/redeem
and enter code TRYAPRIUSPHV. Bam $14 free.
I'm not sure what markets this will work in. The flyer doesn't list
anything specific.
|
|
|
w*******y
发帖数: 60932 | 42 Target (in store only) has Brightboxe DLP Projector on clearance for $89.99,
it was originally $179.99.
You can search in the inventory checker near your zip or city.
I've originally purchased one at target last year and thinking that a
projector for $180? must be junk. Because I've heard others purchased the
discovery projector for $99.99 at FYE or even lower at other stores.
Needlessly to say, I got it out of curiosity because I've never heard of
this brand before. When I turned it on at home ... 阅读全帖 |
|
w*******y
发帖数: 60932 | 43 Strawberry is backordered but other are available
add myofusion 5lbs protein to your cart
add code
BMSM or GNCAPP20
and bam
cheap VERY good tasting, better than ON, Dymatize or others
for around $103 + tax
you can ever do mr rebate too if you want for 10% off, i did an order
similar to think 2 days ago and received my 10lbs but ordered 20lbs today
including 1 Combat Powder Triple Berry
|
|
w*******y
发帖数: 60932 | 44 I just got this in the email, I was skeptical but when I actually clicked it
and opened it
and bam! surprise a $3 off any purchase coupon, the code seems generic and
its valid in store only
I've attached a PDF of it as well.
I noticed you can change location so to the weekly ad located near you, so
it looks its for that store only ( depending on where you go )
|
|
w*******y
发帖数: 60932 | 45 Link:
http://www.microcenter.com/single_product_results.phtml?product
Microcenter B&M has a refurbished Xbox 360 120GB HD for only $9.99!
This is perfect for tearing apart and putting into a Xbox 360 4GB slim model.
Why pay $100 for a new 250GB when you can have a 120GB for $10?
I recently bought the 4GB Xbox 360 slim only to find out that it will NOT
play the old Xbox games (even the ones that are compatible) without an HD.
Well, I didn't want to pay $100 for a HD just play some old Xbox games... 阅读全帖 |
|
w*******y
发帖数: 60932 | 46 Office Depot currently has the Trend Micro Titanium Internet Security 2012 1
User for FAR
++ Advertised as "FREE After $3 Instant, $30 Mfr. Mail-In & $20 Mfr.
Current User
Link:
http://iway.org/9572641
Price match it to Sears
Link:
http://iway.org/9572651
They have it for 14.11 , My rep on chat somehow said was for $11. something
so he issued me a $40 credit.
STEPS:
PLACE ORDER FIRST
AFTER IT SHIPS, CHAT WITH A REP TO GET PRICE MATCH
SUBMIT FOR REBATES USING ORIGINAL OFFICE DEPOT RECEIPTS
BAM $4... 阅读全帖 |
|
N***i
发帖数: 2063 | 47 Best-Rated Financial Stocks Updated June 23, 2010
http://www.nasd100.com/2010/06/bestrated-financial-stocks-updated-june-23-2010.html
Ranking | Company (Ticker) | Average Rating Value | Average Rating
1 IRSA Inversiones Representaciones (ADR) (NYSE:IRS) 1.00 Strong Buy
2 Primus Guaranty, Ltd. (NYSE:PRS) 1.00 Strong Buy
3 China Life Insurance Company Ltd. (ADR) (NYSE:LFC) 1.00 Strong Buy
4 National Bank of Greece (ADR) (NYSE:NBG) 1.00 Strong Buy
5 HDFC Bank Limited (ADR) (NYSE:HDB) 1.00 ... 阅读全帖 |
|
w***y
发帖数: 2537 | 48 【 以下文字转载自 Stock 讨论区 】
发信人: ll111 (Stealth), 信区: Stock
标 题: Events and ER for week August 2-6
发信站: BBS 未名空间站 (Sun Aug 1 22:47:17 2010, 美东)
Monday, Aug. 2
10 a.m.: ISM Manufacturing index on business activity in July, released by
the Institute for Supply Management.
10:15 a.m. Federal Reserve Chairman Ben Bernanke speaking on "challenges for
the economy and state governments."
4 p.m. Treasury Secretary Timothy Geithner speaking on the next steps for
financial reform.
Tuesday, Aug. 3
8:30 a.m.: P... 阅读全帖 |
|
|
|
