Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics

• DOI: 10.1007/s00251-014-0820-3
• Publication Date: 2014-12-12T06:48:07Z
• Authors: Wouter J. Veneman; Jan de Sonneville; Kees-Jan van der ...; Anita Ordas; Zaid Al-Ars; Annemarie H. Meijer; Herman P. Spaink
• Keywords: Identification

We present a RNA deep sequencing (RNAseq) analysis of comparison the transcriptome responses to infection zebrafish larvae with Staphylococcus epidermidis and Mycobacterium marinum bacteria. show how our developed GeneTiles software can improve RNAseq approaches by more confidently identifying large set markers upon these For data currently, programs such as Bowtie2 Samtools are indispensable. However, that designed for LINUX environment require some dedicated programming skills have no options visualisation resulting mapped sequence reads. Especially sets, this makes time consuming difficult non-expert users. applied previously published newly obtained datasets model, we shown applicability approach also other organisms comparing mammalian study. In addition, implemented DEXSeq module in identify genes, glucagon A, differentially spliced under conditions. data, has led possibility size sets could be efficiently compared without using problem-dedicated programs, leading quick identification marker sets. Therefore, will highly useful analyses which well-characterised genomes available.