Wayne:High Throughput Sequencing Resources: Difference between revisions
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== High throughput (HT) datatypes and workflow == | == High throughput (HT) datatypes and workflow == | ||
bcl | File formats and conversions <br> | ||
<ul> | |||
Deplexing <br> | <li> bcl | ||
<li> qseq | |||
<li> fastq | |||
<li> | |||
</ul> | |||
<br> | |||
Deplexing using barcoded sequence tags<br> | |||
<ul> | |||
<li> Editing (or hamming) distance | |||
</ul> | |||
<br> | |||
Quality control <br> | |||
<ul> | |||
<li> Fastx tools | |||
<li> Using mapping as the quality control for reads | |||
</ul> | |||
<br> | |||
Trimming and clipping <br> | Trimming and clipping <br> | ||
<br> | |||
Assembly (by reference or de novo) <br> | Assembly (by reference or de novo) <br> | ||
<br> | |||
<u>Platform and read type</u><br> | <u>Platform and read type</u><br> | ||
<ul> | <ul> | ||
| Line 34: | Line 51: | ||
<li> Genominator (Bullard et al. 2010) | <li> Genominator (Bullard et al. 2010) | ||
</ul> | </ul> | ||
== R basics == | == R basics == | ||
Revision as of 16:48, 15 February 2013
High throughput (HT) datatypes and workflow
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
Assembly (by reference or de novo)
Platform and read type
- Illumina single-end vs. paired-end
- 454 Roche
- SOLiD
- MiSeq
- Ion Torrent
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)
