Wayne:High Throughput Sequencing Resources: Difference between revisions
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== Basic server commands (for Sirius) == | == Basic server commands (for Sirius) == | ||
A suggested concentration for a general PCR cocktail: | |||
<table border="1"> | |||
<tr> | |||
<td><b>Command</b></td> | |||
<td><b>Usage</b></td> | |||
</tr> | |||
<tr> | |||
<td>pwd</td> | |||
<td>Print working directory (your current location</td> | |||
</tr> | |||
<tr> | |||
<td>cd</td> | |||
<td>Change directories</td> | |||
</tr> | |||
<tr> | |||
<td>ls</td> | |||
<td>List (all contents of current location)</td> | |||
</tr> | |||
<tr> | |||
<td>cd</td> | |||
<td>Change directories</td> | |||
</tr> | |||
<tr> | |||
<td>mkdir</td> | |||
<td>Make directories</td> | |||
</tr> | |||
<tr> | |||
<td>2.5μL</td> | |||
<td>2μL</td> | |||
</tr> | |||
<tr> | |||
<td>1.5-2μL</td> | |||
<td>0.8μL</td> | |||
</tr> | |||
<tr> | |||
<td>1.5-2μL</td> | |||
<td>0.8μL</td> | |||
</tr> | |||
<tr> | |||
<td>1μL</td> | |||
<td>0.4μL</td> | |||
</tr> | |||
<tr> | |||
<td>1μL</td> | |||
<td>0.4μL</td> | |||
</tr> | |||
<tr> | |||
<td>0.1μL</td> | |||
<td>0.08μL</td> | |||
</tr> | |||
<tr> | |||
<td>1μL</td> | |||
<td>1μL</td> | |||
</tr> | |||
</table> | |||
<br> | |||
== R basics == | == R basics == | ||
Revision as of 17:03, 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)
A suggested concentration for a general PCR cocktail:
| Command | Usage |
| pwd | Print working directory (your current location |
| cd | Change directories |
| ls | List (all contents of current location) |
| cd | Change directories |
| mkdir | Make directories |
| 2.5μL | 2μL |
| 1.5-2μL | 0.8μL |
| 1.5-2μL | 0.8μL |
| 1μL | 0.4μL |
| 1μL | 0.4μL |
| 0.1μL | 0.08μL |
| 1μL | 1μL |
