NGS Bioinformatics Workshop 1.2 Tutorial – Sequence Formats, Databases and Visualization Tools
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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
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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 ) - PowerPoint PPT Presentation
Transcript of 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, 2012BioSci room B9242
Facilitator: Richard BruskiewichAdjunct Professor, MBB
Learning ObjectivesLinux revisitedQuick dive into the Open-Bio pool (BioPython)A first look at NGS data:
NCBI short read archiveProcessing NGS: FASTX tool kit et al.Visualization: IGV
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
Do a long listing (ls –l)– dr-x-wxrw- Separated into four sections– (d)(r - x)(- w x)(r w -)
Examples: chmod o+x foo.txt grant ‘execute’ permission to ‘others’ on foo.txtchmod g-rw foo.txt remove ‘read’ and ‘write’ permission from groupchmod ugo+rwx foo.txt grant all rights to everyone
To change the user/group (‘owner’) of a file: chmod ubuntu:ubuntu foo.txt
chmod: change file permissions
directory or file (-)user (owner) group others
• 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++)
a few useful tips…
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“ssh” – Secure Shell
ssh –i private_keypair user@host“scp” – Secure CoPy
ssh –i private_keypair [user@host:]sourcefile [user@host:]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
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
http://hannonlab.cshl.edu/fastx_toolkit/
Linux, MacOSX or Unix only
Get the precompiled binarywget http://hannonlab.cshl.edu/fastx_toolkit/Ã fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
bunzip2 fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
tar –xvf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar
sudo mv bin/* /usr/local/bin
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 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
http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
Integrative Genomics Viewerhttp://www.broadinstitute.org/igv/
