strand specific RNA-seq mapping for bacterial transcriptomics
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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.
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.
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.
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?