Question: strand specific RNA-seq mapping for bacterial transcriptomics
0
gravatar for kc
5 days 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 • 111 views
ADD COMMENTlink modified 4 days ago • written 5 days 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 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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1272 users visited in the last hour