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

ABSTRACT: We present a RNA deep sequencing (RNAseq) analysis of a comparison of the transcriptome responses to infection of zebrafish larvae with Staphylococcus epidermidis and Mycobacterium marinum bacteria. We show how our developed GeneTiles software can improve RNAseq analysis approaches by more confidently identifying a large set of markers upon infection with these bacteria. For analysis of RNAseq data currently, software programs such as Bowtie2 and Samtools are indispensable. However, these programs that are designed for a LINUX environment require some dedicated programming skills and have no options for visualisation of the resulting mapped sequence reads. Especially with large data sets, this makes the analysis time consuming and difficult for non-expert users. We have applied the GeneTil

SUBMITTER: Veneman WJ 

PROVIDER: S-EPMC4325186 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature