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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

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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