User: biobiu
biobiu • 110
- Reputation:
- 110
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 3 months ago
- Joined:
- 4 years, 8 months ago
- Email:
- y******@gmail.com
Posts by biobiu
<prev
• 40 results •
page 1 of 4 •
next >
0
votes
0
answers
95
views
0
answers
... I've annotated assembled bins using prokka.
Now I want to cluster the genes by function, pathways etc.
I thought to categorize enzymes by ec number. Any recommendations on how to do that for non-enzymatic protein coding genes? ...
written 3 months ago by
biobiu • 110
0
votes
1
answer
143
views
1
answers
Comment:
C: Download EC number tree
... Thanks!
The only thing is missing now is the classification of the upper levels (like Class 1 - oxydoreductase) ...
written 3 months ago by
biobiu • 110
0
votes
1
answer
143
views
1
answers
Comment:
C: Download EC number tree
... Thanks!
I'm not interested in the sequences but in the enzyme annotations. ...
written 3 months ago by
biobiu • 110
2
votes
1
answer
143
views
1
answer
... I want to download for the full EC number tree (with all level) and can't find it.
My purpose is to assign all levels for a list of enzymes (in example for 1.1.1.1 not just to tell that it alcohol dehydrogenase but also to tell that it is oxidoreductase (class 1), Acting on the CH-OH group of donor ...
0
votes
1
answer
1.7k
views
1
answers
... Thanks!
I'll update... I'm really stuck with rarefying metaphlan2. Well I can subsample reads but it will take forever to subsample different cuttoffs but with repeats it will take forever to re-run metaphlan2.
As for the diveristy- observed OTU (species) and shannon can be calculated easily with re ...
written 5 months ago by
biobiu • 110
1
vote
1
answer
1.7k
views
1
answers
... Hi,
Did you find any solution to this problem? Any suggestion on how to compute diversity with followed by metaphlan2?
...
written 5 months ago by
biobiu • 110
3
votes
2
answers
295
views
2
answers
... I'm interested in alpha and beta diversity analysis based on read based and marker gene methods.
Is there any recommendations on tools or pipeline that:
1) Calculates abundance
2) Rarefaction
3) Calculates diversity
*I'm familiar with several tools that calculates relative abundance but moving from ...
written 5 months ago by
biobiu • 110
• updated
3 months ago by
antonioggsousa • 90
0
votes
0
answers
168
views
0
answers
... Hi!
I'll be very thankful for some feedback here..
I've got a binary matrix of samples X traits, so for each sample I know whether a trait exists or not.
Each sample belongs to a group of samples and I want to test which, if any, of the traits appears dis-proportionally in a group.
Some numbers to ...
1
vote
5
answers
529
views
5
answers
... Try CheckM.
Notice that their strain heterogeneity estimation might be a bit confusing ( for me it is counter intuitive). ...
written 6 months ago by
biobiu • 110
0
votes
1
answer
241
views
1
answers
... Its not necessarily low...
1. If it's host metagenomes you might have the host reads. Try mapping to the host genome.
2. If it doesn't help much would try assembly separately to each sample.
3. Remember that the assembly quality is affected by the read length, sequencing depth and the diversity o ...
written 6 months ago by
biobiu • 110
Latest awards to biobiu
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Does mirna-seq is stranded?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Uniquly aligned reads by BWA-mem (MAPQ, and XA tag)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1094 users visited in the last hour