Wayne:High Throughput Sequencing Resources: Difference between revisions
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<ul> | <ul> | ||
<li> Quantifying and annotating aligned reads | <li> Quantifying and annotating aligned reads | ||
<li> <div> [http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html GenomicRanges] </div> | <li><li> <div> [http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html GenomicRanges] </div> | ||
<li> <div> [http://www.bioconductor.org/packages/release/bioc/html/DESeq.html DESeq] </div> | <li><li> <div> [http://www.bioconductor.org/packages/release/bioc/html/DESeq.html DESeq] </div> | ||
<li> <div> [http://www.bioconductor.org/packages/release/bioc/html/edgeR.html edgeR] </div> | <li><li> <div> [http://www.bioconductor.org/packages/release/bioc/html/edgeR.html edgeR] </div> | ||
< | <li> A variety of additional R packages are available for normalizing RNA-Seq read count data and identifying differentially expressed genes (DEG): <br> | ||
<li><li> <div> [http://bioconductor.org/packages/devel/bioc/html/easyRNASeq.html easyRNASeq] (simplifies read counting per genome feature) </div> | |||
<li><li> <div> [http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html DEXSeq] (Inference of differential exon usage) </div> | |||
<li><li> <div> [http://bioconductor.org/packages/release/bioc/html/DEGseq.html DEGseq] </div> | |||
<li><li> <div> [http://www.bioconductor.org/packages/release/bioc/html/baySeq.html baySeq] (also see: [http://www.bioconductor.org/packages/release/bioc/html/segmentSeq.html segmentSeq)] </div> | |||
A variety of additional R packages are available for normalizing RNA-Seq read count data and identifying differentially expressed genes (DEG): <br> | <li><li> <div> [http://bioconductor.org/packages/release/bioc/html/Genominator.html Genominator] (Bullard et al. 2010) </div> | ||
< | |||
<li> <div> [http://bioconductor.org/packages/devel/bioc/html/easyRNASeq.html easyRNASeq] (simplifies read counting per genome feature) </div> | |||
<li> <div> [http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html DEXSeq] (Inference of differential exon usage) </div> | |||
<li> <div> [http://bioconductor.org/packages/release/bioc/html/DEGseq.html DEGseq] </div> | |||
<li> <div> [http://www.bioconductor.org/packages/release/bioc/html/baySeq.html baySeq] (also see: [http://www.bioconductor.org/packages/release/bioc/html/segmentSeq.html segmentSeq)] </div> | |||
<li> <div> [http://bioconductor.org/packages/release/bioc/html/Genominator.html Genominator] (Bullard et al. 2010) </div> | |||
</ul> | </ul> | ||
Revision as of 18:02, 15 February 2013
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 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
- 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
Common objectives of transcriptome analysis:
- Quantifying and annotating aligned reads
- 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)
- baySeq (also see: segmentSeq)
- Genominator (Bullard et al. 2010)
R basics
HT sequence analysis using R (and Bioconductor)