Wayne:High Throughput Sequencing Resources: Difference between revisions
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<div align="right">[http://openwetware.org/wiki/Wayne_Lab Wayne Lab Home]</div> | <div align="right">[http://openwetware.org/wiki/Wayne_Lab Wayne Lab Home]</div> | ||
<div align="right">[http://openwetware.org/wiki/Wayne:Laboratory_Protocols Laboratory Protocols] </div> | <div align="right">[http://openwetware.org/wiki/Wayne:Laboratory_Protocols Laboratory Protocols] </div> | ||
== Sirius Usage (our lab server) == | |||
Sirius is our analytical powerhouse (64 cores, amazing for parallel computing; 512Gb memory; 64 bit file system in the x86_64 configuration) and we have specific locations on the server to do specific jobs. It is stored in a lovely server closet and so the way to access it is though a secure shell (''ssh''). Your username and password are obtained through our IT staff. Once you have logged on, there are a series of commands and "server etiquette" you will need to follow. | |||
<u>Login</u> | |||
*$ ssh user@sirius.eeb.ucla.edu | |||
*$ slogin user@sirius.eeb.ucla.edu | |||
*to learn about the server: | |||
**$ uname -a | |||
<u>Structure</u> | |||
*Your home (user) director | |||
**/home/user | |||
*Location of installed programs | |||
**/usr/local/bin | |||
**/opt/ | |||
<br> | |||
<div align="right">[http://openwetware.org/wiki/Wayne:High_Throughput_Sequencing_Resources Top]</div> | |||
<div align="right">[http://openwetware.org/wiki/Wayne_Lab Wayne Lab Home]</div> | |||
== Basic server commands (for Sirius) == | == Basic server commands (for Sirius) == |
Revision as of 16:07, 19 February 2013
Sirius Usage (our lab server)
Sirius is our analytical powerhouse (64 cores, amazing for parallel computing; 512Gb memory; 64 bit file system in the x86_64 configuration) and we have specific locations on the server to do specific jobs. It is stored in a lovely server closet and so the way to access it is though a secure shell (ssh). Your username and password are obtained through our IT staff. Once you have logged on, there are a series of commands and "server etiquette" you will need to follow.
Login
- $ ssh user@sirius.eeb.ucla.edu
- $ slogin user@sirius.eeb.ucla.edu
- to learn about the server:
- $ uname -a
Structure
- Your home (user) director
- /home/user
- Location of installed programs
- /usr/local/bin
- /opt/
Basic server commands (for Sirius)
Here is a list of commonly used linux commands:
Command | Usage |
ssh username@sirius.eeb.ucla.edu | Secure shell login to the Sirius server |
logout (or control+D) | Logout of the Sirius server |
pwd | Print working directory (your current location |
ls | List (all contents of current location) |
ls options | ls -a (hidden files), ls -l (long/detailed list), ls -t (sorted by time modified instead of name) |
cd /give/path | Change directories |
cd .. | Go up one directory |
mkdir directoryName | Make a new directory |
rmdir directoryName | Remove directory (must be empty)...Remember that you cannot undo this move! |
rmdir -r directoryName | Recursively remove directory and the files it contains...Remember that you cannot undo this move! |
rmdir filename | Remove specified file...Remember that you cannot undo this move! |
head filename | Print to screen the top 10 lines or so of the specified file |
tail filename | Print to screen the last 10 lines or so of the specified file |
more filename | Allows file contents or piped output to be sent to the screen one page at a time |
less filename | Opposite of more command |
wc filename | Print byte, word, and line counts |
wc [options] filename | -c (bytes); -l (lines); -w (words) delimited by whitespace or newline |
whereis [filename, command] | Lists all occurances of filename or command |
mv current/path destination/path | Move (akin to cut/paste), to remove the file in the current location |
cp current/path destination/path | Copy (also used to rename files if you keep them in their current path), keeps a copy in the current path |
~/path | Tilde designated a shortcut for the path to your home directory |
nohup commands & | To initiate a no-hangup background job |
screen | To initiate a new screen session to start a new background job |
tar -xzf filename.tar.gz | Decompress tar.gz file |
gzip -c filename >filename.gz | Compress file into tar.gz; the ">" means print to outfile filename.gz |
Here is a list of commonly used linux commands for learning about the CPU utilization:
Command | Usage |
top | Display top CPU processes/jobs and provides an ongoing look at processor activity in real time. It displays a listing of the most CPU-intensive tasks on the system, and can provide an interactive interface for manipulating processes. It can sort the tasks by CPU usage, memory usage and runtime. |
mpstat | To display the utilization of each CPU individually. It reports processors related statistics. |
mpstat -P ALL | The mpstat command display activities for each available processor, processor 0 being the first one. Global average activities among all processors are also reported. |
sar | Displays the contents of selected cumulative activity counters in the operating system |
High throughput (HT) platform and read types
- ABI-SOLiD
- Illumina single-end vs. paired-end
- Ion Torrent
- MiSeq
- Roche-454
- Solexa
CBI Collaboratory
UCLA's
Computational Biosciences Institute Collaboratory hosts a variety of 3-day workshops that provide both a general introduction to genome/bioinformatic sciences as well as more advanced (focus) workshops (e.g. ChIP-Seq; BS-Seq; Exome sequencing). The CBI Collaboratory focuses on a set of publicly available resources, from the web-based bioinformatic tool Galaxy/UCLA (resource for HT workflows and is a central location of a variety of HT tools for multiple platforms and data types), but also tools such as R and Matlab. The introductory workshops do not require any programming experience and the Collaboratory Fellows additionally serve as a counseling resource for data analysis.
File formats and conversions
- blc
- qseq
- fastq
Deplexing using barcoded sequence tags
- Editing (or hamming) distance
Quality control
- Fastx tools
- Using mapping as the quality control for reads
Trimming and clipping
- Trim based on low quality scored per nucleotide position within a read
- Clip sequence artefacts (e.g. adapters, primers)
FASTQC and FASTX tools
BED and SAM tools
GATK variant calling
R basics
HT sequence analysis using R (and Bioconductor)
DNA sequence analysis
RNA-seq analysis
Common objectives of transcriptome analysis:
- Quantifying and annotating aligned reads
- Normalizing RNA-Seq read count data and identifying differentially expressed genes (DEG) (R packages):
- easyRNASeq (simplifies read counting per genome feature)
- DEXSeq (Inference of differential exon usage)
- baySeq (also see: segmentSeq)
- Genominator (Bullard et al. 2010)
- Detection of alternative splice junctions
SOLiD software tools