Generation of files in coverage_data

[lvclark]

I am trying to run tu_subcluster_annotation.R, which requires files in data/coverage_data. However, I can't find any scripts or instructions in the rest of the repository explaining how those files should be created.

Thanks in advance!

[felixgrunberger]

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.

[lvclark]

Great, thank you!

[lvclark]

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 -