What it does
DESeq is a tool for differential expression testing of RNA-Seq data.
DESeq requires:
Genome annotation file in GFF3, containing the necessary information about the transcripts that are to be quantified.
The BAM alignment files grouped into replicate groups, each containing several replicates. BAM files store the read alignments, The program will also work with only two groups containing only a single replicate each. However, this analysis has less statistical power and is therefore not recommended!
Licenses
If DESeq is used to obtain results for scientific publications it should be cited as [1].
References
[1] | Anders, S and Huber, W (2010): Differential expression analysis for sequence count data. |
About formats
GFF3 format General Feature Format is a format for describing genes and other features associated with DNA, RNA and protein sequences. GFF3 lines have nine tab-separated fields:
For more information see http://www.sequenceontology.org/gff3.shtml
SAM/BAM format The Sequence Alignment/Map (SAM) format is a tab-limited text format that stores large nucleotide sequence alignments. BAM is the binary version of a SAM file that allows for fast and intensive data processing. The format specification and the description of SAMtools can be found on http://samtools.sourceforge.net/.
DESeq-hts Wrapper Version 0.5 (Aug 2013)