User: biobiu

gravatar for biobiu
biobiu110
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
Categorizing prokka outputs
... 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? ...
gene written 3 months ago by biobiu110
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 biobiu110
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 biobiu110
2
votes
1
answer
143
views
1
answer
Download EC number tree
... 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 ...
gene written 3 months ago by biobiu110 • updated 3 months ago by genomax78k
0
votes
1
answer
1.7k
views
1
answers
Comment: C: Shotgun rarefactions - metagenomics (microbiome), MetaPhlAn2
... 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 biobiu110
1
vote
1
answer
1.7k
views
1
answers
Comment: A: Shotgun rarefactions - metagenomics (microbiome), MetaPhlAn2
... 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 biobiu110
3
votes
2
answers
295
views
2
answers
metagenomics- read based diversity analysis
... 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 ...
metagenomics written 5 months ago by biobiu110 • updated 3 months ago by antonioggsousa90
0
votes
0
answers
168
views
0
answers
Proportion of traits in several groups
... 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 ...
propotion test fisher's exact test forum written 6 months ago by biobiu110 • updated 6 months ago by ATpoint29k
1
vote
5
answers
529
views
5
answers
Answer: A: Genome assembly statistical tools
... Try CheckM. Notice that their strain heterogeneity estimation might be a bit confusing ( for me it is counter intuitive). ...
written 6 months ago by biobiu110
0
votes
1
answer
241
views
1
answers
Answer: A: Low value of mapped reads against a metagenomic co-assembly
... 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 biobiu110

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)

Help
Access

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