Resources

Useful tools:

Browser

The Arabidopsis Information Resource

The Arabidopsis Information Portal 

The Arabidopsis DNA methylation data sets 

UCSC Genome Browser

Galaxy

Arabidopsis thaliana Genome Browser Gateway

Bioinformatics tools 

Bedtools: manipilation of aligned-read files

Bowtie: alignment of reads

Bioconductor

Cufflinks

David

MACS: Peak calling

MEME: Motif-discovery

MOSAICS: Peak calling

NGS plot

RSEM: For determing gene-expression from RNA-Seq reads

Samtools

Network analysis tools

Kegg Pathway analysis

STRING