strand specific RNA-seq mapping for bacterial transcriptomics

Question

[kc]

Hi

Was wondering which would be the best mapper for strand-specific RNA-seq mapping for bacterial transcriptomics?

And are there specific flags to indicate?

Thank you.

[Carlo Yague]

I wonder how you would define "best".

Anyway, given how widely used they are, I would say that bowtie2 and BWA are solid choices for procaryotes.

[kc]

For BWA I suppose we should use BWA-MEM but would there be any specific flags required for strand specific paired-end RNAseq reads?

Thank you.

[h.mon]

Map with BWA or Bowtie2 with default parameters - I wouldn't want to perform any strand-specificity filtering at the mapping step, so later I can evaluate if the strand-specific library-prep worked as expected.

[kc]

Thank you all for your comments! It seems like there isn't a lot of open-source pipelines/workflows for bacterial RNAseq. I know of Rockhopper (standalone app but hard to extract mappings, etc to do other analyses) and SPARTA (which does not take strand-specific)

Are there any other bacterial RNA-seq workflows out there?