Data analysis

Here, you can find a description of the workflow using publicly available tools used to basecall, demultiplex, trim, map and count data. Additionally, we comment on custom Rscripts we used to perform the downstream analysis, including quality control, annotation of transcript boundaries, gene body coverage analysis and transcriptional unit annotation.

Table of contents

• Project organisation
• Basecalling and demultiplexing of raw reads
• Read alignment
• Identification and trimming of full-length reads
• Gene abundance estimation
• Quality control
• Detection of transcript boundaries
• Gene body coverage
• Transcriptional unit analysis