Wayne:High Throughput Sequencing Resources: Difference between revisions

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<td>ssh "username@sirius.eeb.ucla.edu"</td>
<td>Secure shell login to the Sirius server</td>
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<td><b>Command</b></td>
<td><b>Command</b></td>
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<td>Copy (also used to rename files if you keep them in their current path), keeps a copy in the current path </td>
<td>Copy (also used to rename files if you keep them in their current path), keeps a copy in the current path </td>
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<td>~''/path''</td>
<td>~''/path''</td>

Revision as of 18:48, 15 February 2013

Basic server commands (for Sirius)

Here is a list of commonly used linux commands:

ssh "username@sirius.eeb.ucla.edu" Secure shell login to the Sirius server
Command Usage
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:


SOLiD software tools


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