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Forum: Metagenomics 11-06-2017, 06:38 AM
Replies: 0
Views: 374
Posted By GUZUMO
calculate genome bins' similarity

Now I got 2 bins from 2 different samples. And I guess these bins belong to the same genus.
I want to see the similarity between them but I wonder how to do it, as there are not only one sequence...
Forum: Bioinformatics 10-02-2017, 07:44 PM
Replies: 3
Views: 524
Posted By GUZUMO
Thank you . But as idba_ud has a parameter...

Thank you .
But as idba_ud has a parameter '--min count' with description 'minimum multiplicity for filtering k-mer when building the graph', I guess maybe what you say is something like this.[?]...
Forum: Bioinformatics 09-27-2017, 07:42 PM
Replies: 3
Views: 524
Posted By GUZUMO
parameter 'seed kmer' of IDBA_ud

I just don't know what's the meaning of it.
Is there anyone explain it for me ?
Thanks !XD
Forum: Metagenomics 06-07-2017, 02:47 AM
Replies: 0
Views: 682
Posted By GUZUMO
Find single copy gene for bacteria and archaea

just as title says, I want to find and download the single copy gene for bacteria and archaea.
I know there is 107 single copy genes for bacteria(OK, actually, I'm not sure) and know nothing about...
Forum: Metagenomics 04-25-2017, 04:09 AM
Replies: 5
Views: 1,130
Posted By GUZUMO
Thanks, So how to understand "Match Rate" and...

Thanks,
So how to understand "Match Rate" and "Error Rate"?
is there a pdf or something that explain the result of bbmap?
Forum: Metagenomics 04-20-2017, 07:09 PM
Replies: 5
Views: 1,130
Posted By GUZUMO
yes,is there something wrong? thx

yes,is there something wrong?
thx
Forum: Metagenomics 04-20-2017, 03:06 AM
Replies: 5
Views: 1,130
Posted By GUZUMO
how to count the mapped reads with bbmap?

hello, I have assembled paired reads with Megahit, and now I want to know how many reads are uesd to make up those contigs(reads%).
I have tried bbmap and find this in STR:
Pairing data: ...
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