Question: Seed and Kegg analysis in Megan 5
gravatar for simang5c
10 months ago by
simang5c10 wrote:

Hi everyone

I have a BlastNT.xml file and I tried to perform KEGG and Seed analysis using the kegg and seed mapping files gi2kegg-Aug2016X-ue.bin, respectively. Since It Is a BlastNT file there is no Ref SEQ Id. I used the GI id.

Setting Min score as 50, Min support 1 and LCA percent 100, I ran the Megan 5 Software. But all I could find after the run was "no hits" and "not assigned" for both Kegg and seed analysis.

Anyone please help me out. I am a newuser of Megan.

Below is the file contents of my BlastNT.xml file <hit_num>1</hit_num> <hit_id>gi|209529865|gb|CP001189.1|</hit_id> <hit_def>Gluconacetobacter diazotrophicus PAl 5, complete genome</hit_def> <hit_accession>CP001189</hit_accession> <hit_len>3887492</hit_len> <hit_hsps> <hsp>

Thanks in advance!

megan ngs metagenomics • 409 views
ADD COMMENTlink written 10 months ago by simang5c10

I did not try using .xml file. I used diamond to searching reads against nr database and used the .daa files.

Megan 5 is old. Try the new Megan community version.

Make sure you chose the right mapping file (e.g., gi2kegg) at the right place (not accesion) on the seed/kegg tabs.

ADD REPLYlink modified 10 months ago • written 10 months ago by shenwei3563.4k
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