Chip seq

何謂ChIP-Seq?

ChIP–seq ( Chromatin immunoprecipitation sequencing )是指染色質免疫沉澱後,所獲得的DNA片段進行高通量定序,並將此片段利用生物資訊的軟體對回至基因體,可以瞭解DNA-binding proteinshistone modifications的狀況,進而得知染色结合的調控因子的相互作用關係。

ChIP-chipChIP-Seq差異?

次世代定序較ChIP-chip提供更高的解析度,較少的雜訊,較少的ChIP-DNA的量,及可偵測的動態範圍及基因體範圍較廣,因此可呈現較真實的基因調控及表觀遺傳學現況。

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如何分析ChIP-Seq資料?

從次世代定序儀所得到的影像檔,會轉換成核苷酸序列,並計算每個核苷酸的錯誤率,將正確性高的序列對到基因體,找到Peak後,與對照組(通常是Input DNA)比較,利用統計學的計算此Enriched region的錯誤率,之後可進行其它的分析。

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如何找到Protein binding site?

DNA是雙股的結構,因此ChIP-Seq是從DNA5’端定序,會對到基因體的正反股,如下圖可看到藍色序列對到的是正股,紅色序列對到的是反股,因序列的數量畫出常態分佈後找到Peak,而兩者高峰處之間為Protein b[……]

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Mapping reads with bwa and bowtie

In this tutorial, we’re going to take a set of Illumina reads from an inbred Drosophila melanogaster line, and map them back to the reference genome. (After these steps, we could do things like generate a list of SNPs at which this line differs from the reference strain, or generate a genome sequence for this fly strain, but we’ll get to that later on in the course.) We are also going to use two different (but popular) mapping tools, bwa and bowtie. Among their differences is that bowtie (while smokin’ fast) does not deal with “gapped” alignments, i.e. it does not handle insertion/deletions we[……]

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英文写作检查软件汇总:人工智能帮你写论文,语法检查(转贴)

熬夜写paper的学渣小公举

如果能有一款人工智能

帮我改论文

就好了

……

没有paper,就没有伤害

我的心愿是

放飞计几,没有paper

3小时前

想太多,呵呵,别做梦了快醒醒

被paper逼疯的三更半夜,你是不是也会发出这样的感叹呢?

别着急,贴心的留学君这就来为大家介绍一些写作(检查、修改)软件:

1.StyleWriter(润色首推)

http://www.editorsoftware.com/downloads/DWSWT.html

此软件可嵌入word使用,主要功能是检查拼写、语法等错误,润色文章。会有关于同义词选择的提示,让文章的表达更加地道。Style进行文章润色的三个主要指标分别为:bog index,ave sentence, passive index。

其中,Bog index代表文章的“可读性”,其定义为 Bog Index = Sentence Bog + Word Bog – Pep

Sentencebog是句子长度决定的,等于平均句长的平方除以最大句长(long sentence limit,软件似乎设定为35个字,有点儿小气)。

而Wordbog则关乎用词,如难词、大词、专词等,也包括被动语态,这些“毛病”的总和乘[……]

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Python Subprocess returns non-zero exit status only in cron

You should try to capture stderr in addition to stdout so that you can find out exactly why the program is failing (assuming it does indeed print some errors for you)


cmd = ['/path/to/casperjs', '/path/to/doSomething.js', 'args']
response = subprocess.check_output(cmd, 
                shell=True,
                stderr=subprocess.STDOUT)

0 ok    126 权限,拷贝一份,并赋予该用户所有的权限

Apache CGI Script Can Cannot Overwrite a File in a Directory it has full permissions

I ran into this due to the “SELinux” configuration. If SELinux is running, you need to explictly enable the ability for Apache to write to files. To use this, you also need to set additional permissions on those directories and files for which you are granting write access.

To determine if SELinux is enabled, execute:

sestatus

To turn on the SE booleans which enabled cgi to write to files:

sudo setsebool -P allow_httpd_anon_write 1
sudo setsebool -P allow_httpd_sys_script_anon_write 1

Then, finally to set the file/directory “SELinux security context type” to a “system” read/wri[……]

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BACTERIAL GENOMICS TUTORIAL (repost)

[Originally posted by Kat on her BacPathGenomics blog, April 2013]

This is a shameless plug for an article and accompanying tutorial I’ve just published together with David Edwards, my excellent MSc Bioinformatics student from the University of Melbourne. It’s currently available as a PDF pre-pub from BMC Microbial Informatics and Experimentation, but the web version will be available soon. The accompanying tutorial is available here.

The idea for this came from discussions at last year’s ASM (Australian Society of Microbiology) meeting, where it was highlighted that there was a lack of[……]

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POPULATION GENOMICS OF KLEBSIELLA (Repost)

https://holtlab.net/2015/06/23/population-genomics-of-klebsiella/

Well, after almost 6 years, our Klebsiella pneumoniae genomics paper is finally out!

It’s a beast of a thing and there are still a million and one questions to address just from this one data set. For those interested in looking at the data for themselves, the raw reads are available under accessionERP000165, the assemblies are in Sylvain Brisse’s Klebsiella pneumoniae BIGSdb at the Pasteur Institute, and the tree + metadata are available for your interactive viewing pleasure in MicroReact.

The paper itself is open access[……]

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TOOLS FOR BACTERIAL COMPARATIVE GENOMICS

Yesterday I spoke at a workshop for JAMS TOAST (Sydney’s Joint Academic Microbiology Seminars – bioinformatics workshop)… I was asked to cover tools for comparative genomics, so I put together a list of the tried and tested programs that I find most useful for this kind of analysis. So here is the list.

First, a few caveats…

These are mostly tools with a graphical user interface (mostly Java based)… this means they should be pretty accessible to most users, however if you want to do analyses that are a bit more custom or niche, you will have to get your hands dirty and use the commandline (w[……]

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shell脚本-定时执行任务

在linux系统下,我们经常需要定时执行一些固定的任务,比如说服务器每天定时将数据进行备份,但是又不希望人工来操作,因为这样不仅效率低而且又浪费人力资源,我们可以使用shell脚本来配合crontab命令实现定时任务

centos重启命令:

  • reboot
  • shutdown -r now 立刻重启(root用户使用)
  • shutdown -r 10 过10分钟自动重启(root用户使用)
  • shutdown -r 20:35 在时间为20:35时候重启(root用户使用)

Linux centos关机命令:

  • halt 立刻关机
  • poweroff 立刻关机
  • shutdown -h now 立刻关机(root用户使用)
  • shutdown -h 10 10分钟后自动关机
  • 如果是通过shutdown命令设置关机的话,可以用shutdown -c命令取消重启。

实现定时任务crontab

  • 查看当前是否有定时任务
crontab -l
  • 删除定时任务
crontab -r
  • 每个一分钟向/CCoder/aaa.txt写入aaaaa数据
*/1 * * * * echo "aaaaa" >> /CCoder/aaa.txt
  • 定时执行脚本
[......]

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CentOS 7通过Firewall开放防火墙端口

发现在CentOS 7上开放端口用iptables没效果(或者是sodino没找到正确的命令)…
使用firewall-cmd开放端口则立即就生效了。
见下操作:

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firewall-cmd –state //查看运行状态
// 开放1024的端口
firewall-cmd –add-port=1024/tcp permanent
// 重载生效刚才的端口设置
firewall-cmd –reload

效果见下图:
firewall

firewall常用命令如下:

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常用命令介绍
firewall-cmd –state ##查看防火墙状态,是否是running
firewall-cmd –reload ##重新载入配置,比如添加规则之后,需要执行此命令
firewall-cmd –get-zones ##列出支持的zone
firewall-cmd –get-services ##列出支持的服务,在列表中的服务是放行的
firewall-cmd –query-service ftp ##查看ftp服务是否支持,返回yes或者no
firewal[……]

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