RNAseq
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:[http://seqanswers.com/forums/archive/index.php/t-11138.html Informative Q&A for bacterial RNA-seq processing] (GFF file for HTseq-count) | :[http://seqanswers.com/forums/archive/index.php/t-11138.html Informative Q&A for bacterial RNA-seq processing] (GFF file for HTseq-count) | ||
| - | GFF format | + | ::[http://biowiki.org/GffFormat GFF format] |
| - | GFF is a format for locating & describing genes and other localized features associated with DNA, RNA and Protein sequences. | + | :::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) | + | :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 ::reference: PMID 18516045 | |
| + | :FPKM (fragments per kilobase per million reads) | ||
Revision as of 12:07, 12 May 2012
External links
- 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.
- GFF format
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 ::reference: PMID 18516045
- FPKM (fragments per kilobase per million reads)
