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

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.

rna-seq • 411 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by kc0
1

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 11 months ago • written 11 months ago by Carlo Yague4.3k

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 11 months 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 11 months ago by h.mon21k

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 11 months ago by kc0
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