User: biobiu
biobiu • 110
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Posts by biobiu
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... 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 11 days ago by
biobiu • 110
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... Hi,
Did you find any solution to this problem? Any suggestion on how to compute diversity with followed by metaphlan2?
...
written 12 days ago by
biobiu • 110
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... 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 16 days ago by
biobiu • 110
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... 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 ...
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... Try CheckM.
Notice that their strain heterogeneity estimation might be a bit confusing ( for me it is counter intuitive). ...
written 6 weeks ago by
biobiu • 110
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... 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 weeks ago by
biobiu • 110
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... Hi,
I've ran metaphlan2 on shotgun metagenomics sequencing data and want to perform diversity (alpha and beta) analysis.
Is there some tools allows calculating alpha diversity metric to each sample (like shannon), and beta-diversity metrics bewteen pairs of samples (like jaccard or bray curtis).
I ...
written 6 weeks ago by
biobiu • 110
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... We assume that we have un-characterized species of bacteria and non-bacterial genomes. ...
written 6 weeks ago by
biobiu • 110
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... Thanks. Yes I've seen, we think on a way to estimate abundance without using marker genes.
...
written 6 weeks ago by
biobiu • 110
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... Hi,
We performed shotgun metagenomics for dozens of stool samples. Next, we assembled the reads into contigs and binned the contigs to reconstruct the genomes.
We want to use the reconstructed metagenomes in order to calculate the abundance of the microbes they represent in all samples.
1. Is t ...
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