Fail to install DESeq2 Ubuntu 13.04

After trying to install the DESeq2 library

> source("http://bioconductor.org/biocLite.R")
> biocLite("DESeq2")

I got a error because of a cascade of dependencies

DESeq2 <- genefilter <- annotate <- XML

Unfortunately biocLite could not resolve this cascade because of a external dependency

> install.packages("XML")

 

ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/site-library/XML’

 

The problem was that I dind’t have a system library installed. To solve it a had to run:

> sudo apt-get install libxml2-dev

and run the command again within the R environment :

> biocLite("DESeq2")

And everything gone well… Thats it

How to Play ARF file on Ubuntu 12.04-Linux

ARF i.e Advanced Recording Format is a format recorded by NBR (Network Based Recording). For Ubuntu or other Linux versions currently no player is available which can play .arf files i.e WebEx (Player used to play and convert arf and wrf formats) is not supported on Linux based system or Ubuntu 10.04. That’s why to play arf file only one option is available and that is to convert the arf format to mp4 or swf or other simple formats. So you can use a converter tool “NBR2MP4″ to generate mp4 (That we can play Using VLC player) file from arf.

NBR2MP4 is a simple tool and converter that can be used to convert arf formats to mp4 formats. You can install it from command line in few steps (It’s very simple).

Download arf converter for Ubuntu 10.04 and other Linux distros

Download nbr2mp4 from repository from or from here.

Install ARF converter on Ubuntu 10.04 or on linux

1. After downloading the nbr2mp4.tar file, extract it to any directory e.g extra_softwares. It will create a directory nbr2_mp4 and a script file nbr2mp4.sh.

2. Then Make the file nbr2mp4.sh executable by typing this command on the terminal

$ chmod +x ./nbr2mp4.sh

3. Next,Install the converter by typing the command

$ ./nbr2mp4.sh

Type the directory where you want to install the software[/home/rkjha/extra_softwares]:

Extracting files…
Installation is complete.

When it will ask “Type the directory where you want to install….” then just hit enter to install in the current directory(extra_softwares).

4. That’s All…You have installed the arf to mp4 converter successfully..

Converting ARF format to MP4: Ubuntu-Linux

Now,first go to the directory nbr_2mp4 created in extra_softwares(The Directory where you installed the nbr2mp4).next,use the following command to convert format

./nbr2mp4 SOURCE [MP4-DIRECTORY] [FPS]

Where SOURCE means the name of the arf file which you want to convert and don’t forget to specify pathname if it is in the different directory. MP4-DIRECTORY stands for the output file i.e filename .mp4, it’s name will be same as arf file except the extension of .mp4 (Use ./ to generate in the same directory as of input file). In FPS (Frame Per Second) field you can specify between 3 to 10 (Default value is 5). The quality of the mp4 file (output file) is directly proportional to the FPS.

Thanks to blog.sudobits.com

Install Windows 7 from a pen-drive

Hi folks,

 

Some weeks ago I needed to install a Windows 7 in a machine but I didn’t want to burn a DVD only for this, so I decided to search a way to do it using a pen-drive and I found, it is also very usefull in hardwares with no optical drive like Ultrabooks. Here is the way:

Requirements:
- A pen-drive with at least 4Gb
- An windows installation (May be a ISO image file, but in this case you must use the PowerISO in step 3 to extract files to copy them to the pen-drive once copy the whole image wont work)

 

First step: Format the pen-drive to NTFS file system and make it bootable
There is lots of ways to do it:
- In Windows you can use the HP USB Disk Storage Format Tool
- In Linux I suggest the Gparted

Remember to check the option to make the device bootable

 

Second step: Create a boot area

- Open the Windows terminal (type cmd in start menu and execute the cmd.exe)

- Execute the command

bootbootsect /nt60 <USB_device_letter>:

 

Where USB_device_letter is the name of the USB pen drive device (usually D but here in our case is J), dont forget the :

 

If everything goes right, you should see a message like this:

Step three: Copy Windows files to pen-drive

Simple copy the files from DVD to pen-drive (If you are using a image file, like I said earlier you must use the PowerISO to extract the files to a temporary directory and then move it to the pen-drive.

Now it is done and ready to install, the only thing you still may to do is to change the boot sequence (change BIOS configuration to first search from USB drive prior the Hard Disk, usually use F2 or ESC to access BIOS while machine is booting.

 

That’s it folks, hope it helps someone.

 

Bye

Ubuntu 12.04 sidebar auto-hide

Hi folks,

 

Some days ago I decided to update my ubuntu 11.04 to 12.04 and first thing I noticed was the change in the sidebar settings, the side-bar responsiveness was decreased and auto-hide performance became bad.  After a while googling I found a solution the Unsettings, with it is possible to change lots of settings.

For install the software you must add a repository, because the software is not in the official Ubuntu repositories.

 

sudo add-apt-repository ppa:diesch/testing

 

now, update repository list and install software:

 

sudo apt-get update && sudo apt-get install unsettings

 

With this visual tool, you can easily change the settings to your preferences

 

 

Once you chosen the settings, press the engine button to apply settings

 

Thats it folks, hope you enjoy…

 

Skype icon disappeared

Hi folks,

 

Today I will explain how did I do to show the Skype icon in the tray after it  disappeared in ubuntu 11.10 upgrade.

The problem it that when I click in the close button I can’t get the Skype window again unless I kill it in terminal and restart it.

The solution I founded here is this Ubuntu forum thread.

The problem and solution is that, some applications can be whitelisted as being allowed to put an icon there.

 

On terminal:

 

gsettings get com.canonical.Unity.Panel systray-whitelist

 

gave me: ['JavaEmbeddedFrame', 'Wine', 'scp-dbus-service', 'Update-notifier', 'Skype']

So then skype must be added to the whitelist. So add skype like below:

 

gsettings set com.canonical.Unity.Panel systray-whitelist “['JavaEmbeddedFrame', 'Wine', 'scp-dbus-service', 'Update-notifier', 'Skype']”

 

Now the icon should appear in the clock bar like this:

 

 

If you want skype to start at login, and sit in the tray, you need another little trick because the whitelist only works if skype is started manually after login. Add this to the startup list:

gnome-panel –replace

 

And it all works perfectly, hope it works for you too.

 

Bye

Using SSH for access a webpage with a different IP

Hi folks,

 

Today I had the a problem for downloading a article from a academic magazine. Usually this websites uses your IP to allow/deny the restrict area use, the problem is that I am at home and don’t want to go to work just to download it.

 

You can discover the IP that you are using here

 

Here is my IP WITHOUT proxy:

 

 

The solution:

Use the SSH for access the webpage with my Work’s IP

 

How to do it?

On terminal:

ssh -p <ssh_port> -D <port_to_proxy_on_localhost> <user>@<ip_to_use>

Here is a axample:

ssh -p 22 -D 8080 my_user@143.107.223.XXX

 

On browser (firefox) go to (you can also do it in chrome or by Ubuntu proxy settings):
Edit -> Preferences -> Advanced -> Network -> Settings


and than setup “Manual Proxy Configuration” and set SOCKS HOST like 127.0.0.1 and PORT like the port you choosed (in this this case 8080), then click OK


 

Here is my IP WITH proxy

Now you can surf in the web using the Work’s IP and get the same permissions from websites as if you where there.

That’s it folks. Hope you enjoy

Bye

GSM, EDGE, WCDMA, GPRS, HSDPA – Conexão de dados Samsung Galaxy

Pessoal,

 

 

Tempos atrás estava com dúvida sobre a velocidade da conexão de dados pois não entendia as siglas (E, 3G, H) que apareciam na tela no meu celular ao lado do sinal da operadora e também não encotrava no manual do produto e após algum tempo pesquisando achei o significado.

  • G    (GPRS – General Packet Radio Service)→ Primeira versão de transmissão de dados pelo sistema GSM. Suporta uma conexão dados de 40 a 60 kbps.
  • E    (EDGE – Enhanced Data rates for GSM Evolution) → geralmente é classificada como um padrão 2,75G pois é uma melhoria feita nas redes 2,5G (GPRS), introduzida inicialmente nos EUA por volta de 2003. Suporta uma conexão da dados até 384 kbps
  • 3G  (UMTS – Universal Mobile Telecommunications Service) → é uma das tecnologias de terceira geração, suporta uma conexão de até 2 Mbps para comunicações em ambientes internos e pelo menos 144 kbps para ambientes externos
  • H    (HSDPA – High-Speed Downlink Packet Access) → geralmente é classificada como um padrão 3,5G pois é uma melhoria feita através de um upgrade de software nas redes 3G (UMTS),  que suporta taxas de conexão de até 10 Mbps

 

É isso pessoal

 

Abraços

Mate Pair and Paired-End Sequencing – Illumina

Hi folks,

 

 

Today I will post my recurring question about the differences on Mate Pair and Paired-End Sequencing technologies used in Next-Gen sequences.

 

Unfortunately because of technology limitations you can not read long reads, just it their ends (from 35 to 100 bp depending of the chemical and sequencer), to workaround this serious limitation, it was designed this two methodologies.

 

First of all my sources was the own Illumina Website, here is the link for Mate Pair and the link for the Paired-End Seq.  As appear in the website and many articles, these technologies are very useful when you deal with De Novo Sequencing (Assembly a entire Genome) or repetitive parts of genome, why once you have a well aligned sequence and you know the distance between the two sequences you can use the first one as a anchor to determine the second sequence position.  I think the easiest one, is the Paired-End so I will start with it.

I recommend looking at this video for those who know nothing about Illumina technology.

 

Paired-End

 

Paired-End sequecing

It is a modification of the shotgun sequencing(where your sequences have no pairs)

Once you have the DNA fragmented in 200-500 bp, you add adapter in both ends of the sequence of interest (A1 and A2),

In the forth step you generate clusters (spots on flowcell of  same sequences  made by amplification).

Finally after the cluster generation you go to sequencing step (fifth and sixth steps) where using modified dNTPs and primers for know sequences (SP1 and SP2) you read the reads by light signals.

Because you know in the preparation you made sequences of know distance you can/must input this information in your aligner or assembler (depend on your application), because its a very helpful information that will make these softwares to make less mistakes.

Remember that the orientation of a pair of reads (R1/R2) must appear in the aligner output like

(→←) respectively.

 

 

 

 

 

 

 

 

Mate Pair

Mate Pair sequecing

In the mate pair the sequence fragmentation is made in bigger fragments (2-5 kb).

A addition of a Biotin in each 5′ ends is done (step 3).

The sequence with correct addition of Biotin will circularize and after a wash, the sequencing with non-circularized fragment will be thrown away (step 4)

In step 5 and 6, the circularized fragments will be cutted with the biotin in the middle and size-selected (400-600 bp).

And than the sequencing is done normally: adapter with primer sequence addition (step 7), the fragments will be spoted and clutered (step 8), and sequencing (step 9 and 10).

Because you know in the preparation you made sequences of know distance you can/must input this information in your aligner or assembler (depend on your application), because its a very helpful information that will make these softwares to make less mistakes.

Remember that the orientation of a pair of reads (R1/R2) must appear in the aligner output like

() respectively.

 

 

 

 

 

 

 

 

 

 

 

 

Thats it folks, I hope you enjoyed.

 

Bye