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] | ||
:[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. |
+ | :::[http://www.sequenceontology.org/gff3.shtml GFF3 spec] - 9 columns | ||
- | + | ==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 PMID 18516045 | |
+ | |||
+ | ;FPKM (fragments per kilobase per million reads) |
Latest revision as of 03:03, 27 January 2013
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.
- GFF3 spec - 9 columns
- 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 PMID 18516045
- FPKM (fragments per kilobase per million reads)