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)