Genome/Transcriptome databases: JGI; NCBI; RDP (rRNA database)
Mapping-based packages: Bowtie (manual); Bowtie2 (manual); Tophat, Galaxy-based
Map visualization packages: IGV
Other RNAseq packages: Sam Tools (instruction); Picard (instruction); Cufflinks (manual)
Mapping-based packages: Bowtie (manual); Bowtie2 (manual); Tophat, Galaxy-based
Map visualization packages: IGV
Other RNAseq packages: Sam Tools (instruction); Picard (instruction); Cufflinks (manual)