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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::[http://biowiki.org/GffFormat 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== | ==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 | + | :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) | ;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)
