Generation of files in `coverage_data` about native_rnaseq_microbes HOT 3 CLOSED

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.

from native_rnaseq_microbes.

Great, thank you!

from native_rnaseq_microbes.

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 -

from native_rnaseq_microbes.