Question: Fungal NGS data
0
gravatar for khulan1017
5 months ago by
khulan10170
khulan10170 wrote:

Hello, I got the Fungal NGS data from pacbio, but I stuck with how to analyze my fungal seq-data? For bacterial data, I used Geneious 16srRNA DB but they don't have a fungal database yet. I have no idea how to analyze whole sequence data, it's very big data I can't blast every single contigs.

fungal data analysis ngs • 262 views
ADD COMMENTlink modified 4 months ago by joe.khulan0 • written 5 months ago by khulan10170

What exactly do you have? reads or contigs? What are you looking for? Bacterial contamination or Fungal genomic assembly? What do you have sequenced? Genomic DNA?

ADD REPLYlink written 5 months ago by Buffo1.1k
0
gravatar for joe.khulan
4 months ago by
joe.khulan0
joe.khulan0 wrote:

Hello, yes I have a reads and sequenced genomic DNA from soil and plant root, I'm looking for what kind of bacterial and fungal community in soil and root. I need to know a percentage of bacterial and fungal ratio and whole community identification.

ADD COMMENTlink written 4 months ago by joe.khulan0

You can run Standalone BLAST against Silva DB to see what kind of bacterial and fungal community in your samples. To find percentage of bacterial and fungal ratio and whole community identification you can use QIIME pipeline

ADD REPLYlink modified 4 months ago • written 4 months ago by MSM5570
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