Wayne:High Throughput Sequencing Resources: Difference between revisions
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<td | <td> ''top''</td> | ||
<td | <td>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. </td> | ||
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<td> ''mpstat''</td> | |||
<td>To display the utilization of each CPU individually. It reports processors related statistics.</td> | |||
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<tr> | |||
<td> ''mpstat -P ALL''</td> | |||
<td>The mpstat command display activities for each available processor, processor 0 being the first one. Global average activities among all processors are also reported.</td> | |||
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<td> ''sar''</td> | |||
<td>Displays the contents of selected cumulative activity counters in the operating system</td> | |||
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Revision as of 17:36, 15 February 2013
High throughput (HT) platform and read types
- Illumina single-end vs. paired-end
- 454 Roche
- SOLiD
- MiSeq
- Ion Torrent
File formats and conversions
- bcl
- 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)
DNA sequence analysis
RNA-seq analysis
- Quantifying and annotating aligned reads
- DESeq
- edgeR
A variety of additional R packages are available for normalizing RNA-Seq read count data and identifying differentially expressed genes (DEG):
- easyRNASeq (simplifies read counting per genome feature)
- DEXSeq (Inference of differential exon usage)
- DEGseq
- baySeq (also see: segmentSeq)
- Genominator (Bullard et al. 2010)
Basic server commands (for Sirius)
Here is a list of commonly used linux commands:
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 filename [options] | -c (bytes); -l (lines); -w (words) delimited by whitespace or newline |
whereis [filename, command] | Lists all occurances of filename or command |
mv | Move (akin to cut/paste), to remove the file in the current location; Usage: mv current/path/filename destination/path/filename |
cp | Copy (also used to rename files if you keep them in their current path), keeps a copy in the current path; Usage: cp current/path/filename destination/path/filename |
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 using top and learning about the server usage:
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 |