Question: strand specific RNA-seq mapping for bacterial transcriptomics
gravatar for kc
5 days ago by
kc0 wrote:


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.

rna-seq • 111 views
ADD COMMENTlink modified 4 days ago • written 5 days ago by kc0

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.

ADD REPLYlink modified 5 days ago • written 5 days ago by Carlo Yague3.6k

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.

ADD REPLYlink written 4 days ago by kc0

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.

ADD REPLYlink written 4 days ago by h.mon10k

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?

ADD REPLYlink written 1 day ago by kc0
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