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Sorry that this information is missing.
Coverage files were generated in a strand-specific way (after filtering the BAM according to the their flags) with samtools depth -a -d 0
and include the read depth at each position in the genome.
You can also have a look at https://github.com/felixgrunberger/microbepore/blob/master/Rscripts/operon_analysis.R, which is an updated version of the transcriptional unit analysis.
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Great, thank you!
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To get forward and reverse coverage I ended up doing
samtools view -F 0x10 -h -b results/minimap/${Sample_ID}_sorted.bam | \
samtools depth -a -d 0 -o Native_RNAseq_Microbes/coverage_data/${Sample_ID}_plus_depth.txt -
samtools view -f 0x10 -h -b results/minimap/${Sample_ID}_sorted.bam | \
samtools depth -a -d 0 -o Native_RNAseq_Microbes/coverage_data/${Sample_ID}_minus_depth.txt -
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