Linux相关 « 小生这厢有礼了(BioFaceBook Personal Blog)

change the font size of leaf nodes when generating phylogenetic trees using Bio.Phylo.draw()

axes : matplotlib/pylab axes If a valid matplotlib.axes.Axes instance, the phylogram is plotted in that Axes. By default (None), a new figure is created.

This means that you can load your own axes with your size of choice. For example

import matplotlib import matplotlib.pyplot as plt from Bio import Phylo from cStringIO import StringIO def […]

How to find large files with size in Linux? find and du command example

One of the common problem while working in UNIX is to find large files to free some space. Suppose, your file system is full and you are receiving an alert to remove spaces or if your host is run out of space and your server is not starting up, the first thing you do is […]

Chip-seq流程报告(转贴）

一、摘要

实验旨在了解Chip-seq的基本原理。通过模仿文献《Targeting super enhancer associated oncogenes in oesophageal squamous cell carcinoma》的流程，学会利用NCBI和EBI数据库下载数据，熟悉Linux下的基本操作，并使用R语言画图，用Python或者shell写脚本进行基本的数据处理，通过FastQC、Bowtie、Macs、samtools、ROSE等软件进行数据处理，并对预测结果进行分析讨论。

二、材料

1、硬件平台

处理器:Intel（R） Core（TM）i7-4710MQ CPU @ 2.50GHz 2.50GHz

安装内存(RAM)：16.0GB

2、系统平台

Windows 8.1，Ubuntu

3、软件平台

① Aspera connect ② FastQC ③ Bowtie

④ Macs 1.4.2 ⑤ IGV ⑥ ROSE

4、数据库资源

NCBI数据库：https://www.ncbi.nlm.nih.gov/;

EBI数据库：http://www.ebi.ac.uk/;

5、研究对象

加入H3K27Ac 抗体处理过的TE7细胞系测序数据和其空白对照组

加入H3K27Ac 抗体处理过的KYSE510细胞系和其空白对照组

背景简介：食管鳞状细胞癌（OSCC）是一种侵袭性的恶性肿瘤，本文章通过高通量小分子抑制剂进行筛选，发现了一个高度有效的抗癌物，特异性的CDK7抑制剂THZ1。RNA-Seq显示，低剂量THZ1会对一些致癌基因的产生选择性抑制作用，而且，对这些THZ1敏感的基因组功能的进一步表征表明他们经常与超级增强子结合（SE）。ChIP-seq解读在OSCC细胞中，CDK7的抑制作用的机制。

本文亮点：确定了在OSCC细胞中SE的位置，以及识别出许多SE有关的调节元件；并且发现小分子THZ1特异性抑制SE有关的转录，显示强大的抗癌性。

文章PMID: 27196599

三、方法

1、Aspera软件下载及安装

进入Aspera官网的Downloads界面，选中aspera connect server，点击Wwindows图标，选择v3.6.2版本，点击Download进行下载。

[…]

Dating a node with BEAST2.0

For details, read http://beast2.cs.auckland.ac.nz/index.php/Main_Page and http://beast2.cs.auckland.ac.nz/index.php/FAQ . For any problem, do not hesitate to browse through the list of questions on the BEAST forum https://groups.google.com/forum/#!forum/beast-users .

Exercise description

The exercise is mainly based on the Divergence Dating tutorial, but also includes a few screen captures.

Sequences files for this exercise are taken from a […]

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 […]

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, […]

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 //test.sh #! /bin/bash echo “This is […]

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：

1 2 3 4 5 6 7 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常用命令如下：

1 2 3 4 5 6 7 8 9 10 11 12 13 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 […]

docker 删除images

docker中删除images的命令是docker rmi，但有时候执行此命令并不能删除images

[yaxin@ubox ~]$docker images REPOSITORY TAG IMAGE ID CREATED VIRTUAL SIZE eg_sshd latest ed9c93747fe1 45 hours ago 329.8 MB CentOS65 latest e55a74a32125 2 days ago 360.6 MB [yaxin@ubox ~]$docker rmi ed9c93747fe1 Untagged: ed9c93747fe16627be822ad3f7feeb8b4468200e5357877d3046aa83cc44c6af [yaxin@ubox ~]$docker images REPOSITORY TAG IMAGE ID CREATED VIRTUAL SIZE <none> <none> ed9c93747fe1 45 hours ago 329.8 MB CentOS65 latest e55a74a32125 […]

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