Wayne:High Throughput Sequencing Resources: Difference between revisions
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== High throughput (HT) datatypes and workflow == | |||
bcl file conversion to qseq | |||
Qseq and fastq file conversions | |||
Deplexing | |||
Fastq inspection (quality) | |||
Trimming and clipping | |||
Assembly (by reference or de novo) | |||
Short vs. long reads; single-end vs. paired-end | |||
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) | |||
== R basics == | |||
== HT sequence analysis using R (and Bioconductor) == | |||
<div align="right">[http://openwetware.org/wiki/Wayne_Lab Wayne Lab Home]</div> | <div align="right">[http://openwetware.org/wiki/Wayne_Lab Wayne Lab Home]</div> | ||
Revision as of 16:41, 15 February 2013
Programs, scripts, and work-flow goes here!
High throughput (HT) datatypes and workflow
bcl file conversion to qseq Qseq and fastq file conversions Deplexing Fastq inspection (quality) Trimming and clipping Assembly (by reference or de novo) Short vs. long reads; single-end vs. paired-end 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)
