Question: MEGAN and Kraken for taxonomy classification
0
gravatar for deepthithomaskannan
5.7 years ago by
Canada
deepthithomaskannan320 wrote:

Hi,

I am trying to do taxonomy classification for my unmapped (to reference genome) reads. I tried both Megan (http://ab.inf.uni-tuebingen.de/software/megan5/ ) and kraken(http://ccb.jhu.edu/software/kraken/ ).

In kraken I can use read files directly as the input, whereas in Megan I have to make the blastN file first from the read files to give it as the input.

No plotting tool is readily available for kraken, while Megan already has a plotting tool.

I used bacteria,virus and fungi genomes as reference database.  I am trying to figure out if I can use read files directly as an input to MEGAN so that I can skip the BLASTN step.

I also want to compare the Megan and kraken output.

Thanks,

Deepthi

megan readfile kraken taxonomy • 4.8k views
ADD COMMENTlink modified 5.5 years ago by ramanandan.prabhakaran20 • written 5.7 years ago by deepthithomaskannan320

Which BLASTN step? Please provide some context.

Comparing your two other questions, I think you would be better off if you'd made a single question explaining your premise, what you are looking to achieve and then listing your questions in a specific fashion with relevant context.

EDIT: Restructured your question so it is easier to compartmentalize while reading.

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by RamRS30k
2
gravatar for Phil S.
5.7 years ago by
Phil S.660
Stuttgart, Germany
Phil S.660 wrote:

Hi,

it is not possible to directly input read files into megan, afaik. However, to get a first guess what your reads are depicting using kraken you can use krona-tools (which they also used) in their paper to visualize results.

 

HTH

ADD COMMENTlink written 5.7 years ago by Phil S.660

Thank you Phil. 

Deepthi

ADD REPLYlink written 5.7 years ago by deepthithomaskannan320
0
gravatar for ramanandan.prabhakaran
5.5 years ago by
Canada
ramanandan.prabhakaran20 wrote:

Hi Deepthi,

I am also working on kraken to build my own custom DB. As you mentioned in the above post, you built your database consisting of bacteria, virus and fungi. Even my requirement is to build custom DB with the same three species. 

1) Can you help me with that custom DB?

2) Can I use RefSeq proteins instead of RefSeq genomes to build custom DB?

Cheers,

Ram

 

ADD COMMENTlink written 5.5 years ago by ramanandan.prabhakaran20

hi,

 

kraken can only use AGTC sequences, everything else it will treat as ambigous. So no, you can't you proteins (afaik). The creation of custom databases is really nice explained in the kraken manual (which is, in its whole, a nicely written thing!). The manual can be found here

 

HTH,

 

phil

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Phil S.660
0
gravatar for ramanandan.prabhakaran
5.5 years ago by
Canada
ramanandan.prabhakaran20 wrote:

Thanks Phil for providing me a nice explanation.

I am new to metagenomics field. I would like to generate synthetic reads similar to 454 or Illumina. I figured out MetaSim can generate it. But I have doubt, can we use gene sequences (fasta format) from NCBI as a input to generate synthetic reads instead of genome sequences?

ADD COMMENTlink written 5.5 years ago by ramanandan.prabhakaran20

Move this to a reply on Phil's comment please.

ADD REPLYlink written 5.5 years ago by RamRS30k
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