Wayne:High Throughput Sequencing Resources: Difference between revisions
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== High throughput (HT) | == High throughput (HT) platform and read types == | ||
<ul> | <ul> | ||
<li> Illumina single-end vs. paired-end | <li> Illumina single-end vs. paired-end | ||
| Line 10: | Line 8: | ||
</ul> | </ul> | ||
== File formats and conversions == | |||
<ul> | <ul> | ||
<li> bcl | <li> bcl | ||
| Line 19: | Line 17: | ||
<br> | <br> | ||
== Deplexing using barcoded sequence tags == | |||
<ul> | <ul> | ||
<li> Editing (or hamming) distance | <li> Editing (or hamming) distance | ||
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<br> | <br> | ||
== Quality control == | |||
<ul> | <ul> | ||
<li> Fastx tools | <li> Fastx tools | ||
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<br> | <br> | ||
== Trimming and clipping == | |||
<ul> | <ul> | ||
<li> Trim based on low quality scored per nucleotide position within a read | <li> Trim based on low quality scored per nucleotide position within a read | ||
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<br> | <br> | ||
== DNA sequence analysis == | |||
<br> | <br> | ||
== RNA-seq analysis == | |||
<ul> | <ul> | ||
<li> Quantifying and annotating aligned reads | <li> Quantifying and annotating aligned reads | ||
Revision as of 16:53, 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)
