RNAseq

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	==External links==		==External links==
-	:[http://seqanswers.com/wiki/How-to/RNASeq_analysis RNA-seq analysis HowTo]	+	:[http://seqanswers.com/wiki/How-to/RNASeq_analysis RNA-seq analysis HowTo] - changed to [http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)/RNA]
	:[http://www.bioconductor.org/ Bioconductor]		:[http://www.bioconductor.org/ Bioconductor]
	::[http://www.bioconductor.org/help/workflows/high-throughput-sequencing/ Using Bioconductor for Sequence Data]		::[http://www.bioconductor.org/help/workflows/high-throughput-sequencing/ Using Bioconductor for Sequence Data]

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Revision as of 03:01, 27 January 2013

External links

RNA-seq analysis HowTo - changed to [1]

Bioconductor

Using Bioconductor for Sequence Data

Informative Q&A for bacterial RNA-seq processing (GFF file for HTseq-count)

GFF format

GFF is a format for locating & describing genes and other localized features associated with DNA, RNA and Protein sequences.

Terminology

RPKM (reads per kilobase per million reads) = 10^9 * C / (N * L)

where C = # of mappable reads to a gene (exons), N = total # of mappable reads (size of library), and L = size of gene (bp) or sum of exons PMID 18516045

FPKM (fragments per kilobase per million reads)