This file describes the steps and used programs for the analysis of RNASeq data (TEX+, TEX-, Transcriptome) for H.volcanii. 1) Mapping of reads: Trimmed, clipped and mapped reads for all 3 data sets (TEX+, TEX-, Transcriptome and 3 replicons each). Mapped to the reference genome of H.volcanii. Clipping and trimming: cutadapt version 1.10 [1] based on fastqc reports, version 0.11.4 [2] Mapping: segemehl (version 0.2.0) [3] Processing of reads: samtools, version 1.3 [4] Read coverage for the complete genome was calculated using bedtools overlap, version v2.26.0 [5] 2) DSM analysis We reimplemented DSM as reported in (Dar et al., 2016) using perl scripts and samtools, version 1.3 [4]. Scripts and explanations are given, see README_DSM. 3) Application of Internal Enrichment program In order to see how IE can be used, see the corresponding README. IE was applied to mapped reads of TEX+ data (bam files). 4) Application of Peak calling See peakcallingworkflow.zip and README file inside 5) Comparison of IE and PC - terminator identification Overlapping position resulting from IE and PC were reported using bedtools version v2.26.0 [5]. Positions with a distance of at most 10nt were summarized and the position with the highest coverage was reported. 6) Sequence motif detection Sequence motifs were detected using MEME, version 5.0.1 [6]. For this, sequences 15nt upstream and 5nt downstream of TTS were extracted and used as an input. 7) Structure motif detection Structure search was conducted using graphclust 2.0 within Galaxy [7]. For this, sequences with 100nt upstream and 2nt downstream of TTS were extracted and used as input. 8) Confirmation of 3'UTRs based on transcriptome data bedtools genomecov was used in order to get a genome-wide coverage of transcripts based on transcriptome data. Potential 3' UTR regions were collected and scanned using UCSC tools [8] bedGraphToBigWig and bigWigAverageOverBed. [1] https://cutadapt.readthedocs.io/en/stable/ [2] http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ [3] http://www.bioinf.uni-leipzig.de/Software/segemehl/ [4] http://www.htslib.org/ [5] https://bedtools.readthedocs.io/en/latest/ [6] http://meme-suite.org/ [7] https://github.com/BackofenLab/GraphClust-2 [8] http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads