Question: How to separate sequences of two species from Metagenomics Analysis?
0
gravatar for hafiz.talhamalik
10 months ago by
Pakistan
hafiz.talhamalik220 wrote:

I have sequenced a genomics data. This contains ecoli and naegleria fowleri, and I want to separate both of them so I could assemble naegleria fowleri genome. Any Idea how to separate them from fastq files??

ADD COMMENTlink modified 12 weeks ago by Biostar ♦♦ 20 • written 10 months ago by hafiz.talhamalik220
1

You could try profiling with kraken/centrifuge. I believe they will separate out the reads for you too (I could be wrong).

ADD REPLYlink written 10 months ago by Joe15k

OK I will try that and will let you know.

ADD REPLYlink written 10 months ago by hafiz.talhamalik220
1

In this case you can use fastqscreen or bbbbsplit.sh (module available under BBMap package.

Both the tools will map your raw reads on multiple reference genomes.

NOTE: In this case you have to consider unaligned reads (failed to map on any of your reference genomes) for assembly construction.

ADD REPLYlink modified 10 months ago • written 10 months ago by Nitin Narwade440

oh great.! I think these will serve the purpose.

ADD REPLYlink written 10 months ago by hafiz.talhamalik220

Dear hafiz.talhamalik,

If my suggestion somehow helps you to get an idea for resolving your query, could you please hit on upvote button?

Thank you.

ADD REPLYlink written 10 months ago by Nitin Narwade440

Try mapping to E.coli first, check the coverage (they may share some genes), and assemble with unmapped reads. It may be hard to separate If they share some genes.

ADD REPLYlink written 10 months ago by shenwei3565.0k
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