TT-seq analysis - TU annotation

In this post, we will use R shiny application developed by Shao et al. (1), to annotate transcriptional units in the data. The code for this app is available at TU_filter

The app essentially performs the following steps:
1) binning the genome into 200 bases bins,
2) calculate the strand-specific coverage,
3) divide genome into “transcribed” (transcription units, ThUs) and “not-transcribed” regions using GenoSTAN package,
4) join the resulting TUs by exons (coding regions), assume the rest as ncRNAs.

1) reference genome in gtf format - here I used mm10 latest realease from gencode
2) bam files

1) a graph with number of TUs per class

TUs per class

2) gff3 file with TU intervals


  1. Distinct transcription kinetics of pluripotent cell states. Rui Shao, Banushree Kumar, Katja Lidschreiber, Michael Lidschreiber, Patrick Cramer, Simon J Elsässer. Molecular Systems Biology (2022)18:e10407