Question: strand specific RNA-seq mapping for bacterial transcriptomics
gravatar for kc
9 weeks 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 • 191 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks 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 9 weeks ago • written 9 weeks ago by Carlo Yague3.7k

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 9 weeks 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 9 weeks ago by h.mon12k

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 8 weeks ago by kc0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 639 users visited in the last hour