add swap space

if you run softwares that require a large amount of memory, you need to add more swap space

You have three options: create a new swap partition, create a new swap file, or extend swap on an existing LVM2 logical volume. It is recommended that you extend an existing logical volume.

https://www.centos.org/docs/5/html/Deployment_Guide-en-US/s1-swap-adding.html

tar extract file

tar extract file

http://www.cyberciti.biz/faq/tar-extract-linux/

tar -xvf file.tar

tar -xzvf file.tar.gz 

tar -xjvf file.tar.bz2

things to install for NGS analysis

NCURSE -programming library for text-based user interfaces
 http://codybonney.com/installing-the-ncurses-library-in-centos-6-5/

 sudo yum install ncurses-devel


Cutadapt - adapter sequence trimming
 http://cutadapt.readthedocs.org/en/latest/index.html

Trimmomatic: A flexible read trimming tool for Illumina NGS data
 http://www.usadellab.org/cms/?page=trimmomatic

FastQC - quality check of fastq file
 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Bowtie - short read aligner
 http://bowtie-bio.sourceforge.net/index.shtml
 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Tophat - splice junction mapper for RNA-Seq reads (need Bowtie)
 https://ccb.jhu.edu/software/tophat/index.shtml

samtools - tools for manipulating alignments in the SAM(Sequence Alignment/Map) format,
 http://samtools.sourceforge.net/

picard -  tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF
 http://broadinstitute.github.io/picard/

HTSeq - Python package that provides infrastructure to process data from high-throughput sequencing assays
 http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html

MACS - Model-based Analysis for ChIP-Seq
 http://liulab.dfci.harvard.edu/MACS/

PeakSplitter - Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks
 http://www.ebi.ac.uk/research/bertone/software

R -  free software environment for statistical computing and graphics
 https://www.r-project.org/

IGV - Integrative Genomics Viewer
 https://www.broadinstitute.org/igv/
 (log in required)

centOS 7 installation

see more details in
http://linoxide.com/how-tos/centos-7-step-by-step-screenshots/

1. download centOS 7 iso file
http://www.centos.org/download/
download DVD iso

 * check md5checksum of download iso file to verify complete  file download

2. download win32 disk imager (to make USB booting disk)
http://sourceforge.net/projects/win32diskimager/

3. burn iso image to USB with win32 disk imager  (use 8G USB)

4. boot with USB (go BIOS and select USB for booting)

5. in "software selection"
 select "GNOM Desktop"  and "legacy X window system" in add-ons for selected environment

6. in "installation destination"
 select "I will configure partitioning" and set partitioning

7. set root password & create user account
 * remember root password !!!

8. complete installation and check reboot (remove USB booting disk before reboot)

FTP command

ascii(as)	set transfer mode to ascii mode
binary(bi)	set transfer mode to binary mode
bye	exit ftp
chmod	change file permission
close	close connetion
delete	delete file
get	download file
hash	display file transer status with '#'
help	help
lcd	change working directory
ls	shows file list in the directory
mdelete	delete multiple files
mget	download multiple files
mput	upoad multiple files
open	ftp open
prompt	on/off prompt mode
put	upload file
pwd	show current working directory
quit	exit ftp
rstatus	shows current connection status of remote
rename	change file name
rmdir	remove directory
size	display file size as byte
status	shows current connection status
trace	on/off packet tracing
type	set file transfer mode
verbose	on/off detailed information
?	help
!	move to local computer without disconnect to remote computer. Type 'exit' to move to remote computer

DOS format UNIX format error

when you use text file in both window and UNIX, linux

it could cause file format error because they use different newline


unix  <LF>          (each line ends with LF).
dos  <CR><LF> (each line ends with CR and LF).
mac  <CR>         (each line ends with CR).

CR(Carriage Return) , 0x0D
LF(Line Feed) , 0x0A


so if you use text file, you should check the text file has right format for the OS

you can change file format with text-editer (ex: Ultraedit)

for more information, visit

http://en.wikipedia.org/wiki/Newline

path setup

vi ~/.bash_profile

---------------------------

PATH=/bin:/usr/bin/:/usr/local/bin :/address/want/to/save

export PATH

----------------------------


echo $PATH

source ~/.bash_profile   ( to apply modified path)