rna_seq_counts
Align paired-end RNA-seq reads with BWA-MEM and count reads per feature, with each sample
aligned to its own isolate’s assembly rather than a shared reference.
A single reference can only receive reads from genes it carries, so accessory-genome
transcripts have nowhere to map, and reads from divergent strains map with a bias against
them. Aligning each sample to the assembly it came from avoids both. The workflow also runs
against a single shared reference (`match_mode = "
This is a companion discussion topic for the original entry at github.com/alex-omics/microbial-genomics-wdl/rna_seq_counts