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NGS Bioinformatics Workshop 1.2 Tutorial – Sequence Formats, Databases and Visualization Tools. March 15 th , 2012 BioSci room B9242 Facilitator: Richard Bruskiewich Adjunct Professor, MBB. Learning Objectives. Linux revisited Quick dive into the Open-Bio pool ( BioPython )

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Ngs bioinformatics workshop 1 2 tutorial sequence formats databases and visualization tools

NGS Bioinformatics Workshop1.2 Tutorial – Sequence Formats, Databases and Visualization Tools

March 15th, 2012

BioSci room B9242

Facilitator: Richard Bruskiewich

Adjunct Professor, MBB


Learning objectives
Learning Objectives

  • Linux revisited

  • Quick dive into the Open-Bio pool (BioPython)

  • A first look at NGS data:

    • NCBI short read archive

    • Processing NGS: FASTX tool kit et al.

    • Visualization: IGV


Files and permission
Files and Permission

  • Linux user permissions: owner, group, or others

    • Owner/user is the person who created the file

      • “OWNS” the file / directory

    • Group is a team of people that’s associated together

      • GROUP project / Team work

    • Others is just other people on the server

  • Each file / directory can have it’s permission set to (r)ead, (w)rite, or e(x)ecute


Chmod change file permissions
chmod: change file permissions

Do a long listing (ls –l)

  • dr-x-wxrw- Separated into four sections

  • (d)(r - x)(- w x)(r w -)

    Examples: chmodo+x foo.txt  grant ‘execute’ permission to ‘others’ on foo.txt

    chmod g-rw foo.txt  remove ‘read’ and ‘write’ permission from group

    chmodugo+rwxfoo.txt  grant all rights to everyone

    To change the user/group (‘owner’) of a file:

    chmodubuntu:ubuntu foo.txt

directory or file (-)

user (owner)

group

others


A few useful tips
a few useful tips…

  • Hitting “tab” will auto-complete file or program names (or suggest possible names)

  • Up arrow will let you return to previous commands

  • Editing of text files: “nano” is an easier alternative to “emacs”, but less powerful alternatively, use SSH client to transfer files on your Windows desktop, edit them in Windows, then transfer back BUT: make sure you use a text editor that knows the difference between a Windows and a Linux text file (e.g. Notepad++)


Some more useful basic linux commands
Some more useful basic Linux commands

  • “cd” changes your directory, e.g. ‘cd /usr/local’

  • “man” display manual for command, e.g. ‘man ‘ls’

  • “pwd” tells you the directory you are currently in (= working directory)

  • “history” will list recent commands, enumerated with line numbers. By; typing an exclamation point with the line number (e.g. !123), you can redo the command


Accessing remote servers
Accessing remote servers

  • “ssh” – Secure Shell

    ssh [email protected]

  • “scp” – Secure CoPy

    ssh–iprivate_keypair[[email protected]:]sourcefile [[email protected]:]targetfile

    Where user is the account (default: local user)

    and host is the internet name of the computer (defaults: local host)


Openbio case study biopython
OpenBio Case Study: BioPython

http://biopython.org/wiki/Biopython

http://biopython.org/DIST/docs/tutorial/Tutorial.html


First look at ngs data

NGS Bioinformatics Workshop1.2 Tutorial – Sequence Formats, Databases and Visualization Tools

First look at ngs data


Http www ncbi nlm nih gov sra
http://www.ncbi.nlm.nih.gov/sra/


Http hannonlab cshl edu fastx toolkit
http://hannonlab.cshl.edu/fastx_toolkit/

Linux, MacOSX or Unix only


Get the precompiled binary
Get the precompiled binary

wgethttp://hannonlab.cshl.edu/fastx_toolkit/Ã

fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2

bunzip2fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2

tar –xvffastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar

sudomv bin/* /usr/local/bin


Fastx tool kit i
FASTX tool kit I

  • FASTQ-to-FASTA converter

    • Convert FASTQ files to FASTA files.

  • FASTQ Information

    • Chart Quality Statistics and Nucleotide Distribution

  • FASTQ/A Collapser

    • Collapsing identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)

  • FASTQ/A Trimmer

    • Shortening reads in a FASTQ or FASTQ files (removing barcodes or noise).

  • FASTQ/A Renamer

    • Renames the sequence identifiers in FASTQ/A file.

  • FASTQ/A Clipper

    • Removing sequencing adapters / linkers


Fastx tool kit ii
FASTX tool kit II

  • FASTQ/A Reverse-Complement

    • Producing the Reverse-complement of each sequence in a FASTQ/FASTA file.

  • FASTQ/A Barcode splitter

    • Splitting a FASTQ/FASTA files containing multiple samples

  • FASTA Formatter

    • Changes the width of sequences line in a FASTA file

  • FASTA Nucleotide Changer

    • Converts FASTA sequences from/to RNA/DNA

  • FASTQ Quality Filter

    • Filters sequences based on quality

  • FASTQ Quality Trimmer

    • Trims (cuts) sequences based on quality

  • FASTQ Masker

    • Masks nucleotides with 'N' (or other character) based on quality


Www bioinformatics bbsrc ac uk projects download html
www.bioinformatics.bbsrc.ac.uk/projects/download.html

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/


Integrative genomics viewer
Integrative Genomics Viewer

http://www.broadinstitute.org/igv/


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