RNAseq
From CSBLwiki
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.
- GFF3 spec - 9 columns
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)
