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Burkholderia cenocepacia data RNA-Seq analysis scripts for Sass et al.

Sass, Andrea M. ; Van Acker, Heleen ; Förstner, Konrad U.; Van Nieuwerburgh, Filip; Deforce, Dieter ; Vogel, Jörg ; Coenye, Tom

These shell scripts are part of the publication "Genome-widetranscription start site profiling in biofilm-grown Burkholderia cenocepacia J2315" by Andrea Sass et al. (DOI:10.1186/s12864-015-1993-3).

Please generate a folder "FASTQ" and add the raw sequences in FASTQ format (deposited at ArrayExpress under the accession number E-MTAB-3381) in that folder. The files should be called the following:

  • RNA_BF1_minus_TEX.fq.bz2
  • RNA_BF1_plus_TEX.fq.bz2
  • RNA_BF2_minus_TEX.fq.bz2
  • RNA_BF2_plus_TEX.fq.bz2

To perform the analysis run

./run_analysis.sh

Please make sure that the software is installed and the variable are set accordingly in run_analysis.sh. To install the required software you can use

./install_software.sh

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