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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


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    <subfield code="a">&lt;p&gt;These shell scripts are part of the publication &amp;quot;Genome-widetranscription start site profiling in biofilm-grown Burkholderia cenocepacia J2315&amp;quot; by Andrea Sass et al. (DOI:10.1186/s12864-015-1993-3).&lt;/p&gt;

&lt;p&gt;Please generate a folder &amp;quot;FASTQ&amp;quot; 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:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;RNA_BF1_minus_TEX.fq.bz2&lt;/li&gt;
	&lt;li&gt;RNA_BF1_plus_TEX.fq.bz2&lt;/li&gt;
	&lt;li&gt;RNA_BF2_minus_TEX.fq.bz2&lt;/li&gt;
	&lt;li&gt;RNA_BF2_plus_TEX.fq.bz2&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;To perform the analysis run&lt;/p&gt;

&lt;p&gt;./run_analysis.sh&lt;/p&gt;

&lt;p&gt;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&lt;/p&gt;

&lt;p&gt;./install_software.sh&lt;/p&gt;</subfield>
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