What it does
DESeq2 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
DESeq2 requires:
Genome annotation in GFF file type, 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 DESeq2 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
GFF/GTF format General Feature Format/Gene Transfer 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
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/.
DESeq2-hts Wrapper Version 0.2 (Aug 2013)