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Linux command line exercises for NGS data processing Linux command line exercises for NGS data processing by The purpose of this tutorial is to introduce students to the frequently used tools for NGS analysis as well as giving experience in writing one-liners. Copy the required files to your current directory, change directory ( cd) to the linuxTutorial folder, and do all the processing inside: [uzi@quince-srv2 ~/]$ cp -r /home/opt/MScBioinformatics/linuxTutorial. [uzi@quince-srv2 ~/]$ cd linuxTutorial [uzi@quince-srv2 ~/linuxTutorial]$ I have deliberately chosen Awk in the exercises as it is a language in itself and is used more often to manipulate NGS data as compared to the other command line tools such as grep, sed, perl etc. Furthermore, having a command on awk will make it easier to understand advanced tutorials such as.

In Linux, we use a shell that is a program that takes your commands from the keyboard and gives them to the operating system. Most Linux systems utilize Bourne Again SHell ( bash), but there are several additional shell programs on a typical Linux system such as ksh, tcsh, and zsh. To see which shell you are using, type [uzi@quince-srv2 ~/linuxTutorial]$ echo $SHELL /bin/bash To see where you are in the file system: [uzi@quince-srv2 ~/linuxTutorial]$ pwd /home/uzi/linuxTutorial List the files in the current directory: [uzi@quince-srv2 ~/linuxTutorial]$ ls data Now try different commands from the sheet given below. Linux Commands Cheat Sheet • File System ls — list items in current directory ls -l — list items in current directory and show in long format to see perimissions, size, and modification date ls -a — list all items in current directory, including hidden files ls -F — list all items in current directory and show directories with a slash and executables with a star ls dir — list all items in directory dir cd dir — change directory to dir cd.

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Gives some good suggestions that might improve your overall download speed. Just enter the maximum upload speed of your connection, and the calculator will give you your recommended upload speed (), maximum connections per torrent, and some other settings. The calculator can be used for every torrent client.

The maximum upload speed is by far the most important setting. It might sound strange to some, but you should always cap your upload speed to reach the best download speeds.

Your connection is (sort of) like a pipeline (or tube if you prefer), if you max out your upload speed the pipe will be fully used, which means there’s not enough space left for the files you are downloading. The calculator recommends to set it at 80% of your maximum, I agree with that. People with high-speed connections might go a bit higher, and set is at 85% or even 90%.

Some people find that when they are seeding, browsing the web becomes sluggish. This is due to a badly configured upload speed in their BitTorrent client. When you have the correct upload speed entered into your client, browsing the web is noticeably quicker and seeding becomes almost transparent. How to configure your maximum upload speed? UTorrent: options > preferences > connection Azureus: tools > options > transfer Bitcomet: Here at TorrentFreak we also wrote some post about optimizing BitTorrent download speeds, might be worth the read if you want to know more. Read more on optimizing your BitTorrent Speed.• • •.

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