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Phyloseq Weighted Unifrac Ordination Error

unifrac phyloseq pcoa ordination ape written 9 months ago by mzmd4 • 0 • updated 8 months ago by Kevin Blighe ♦ 30k

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838

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Bacterial phylogeny download for a list of species

unifrac metagenomics tree written 17 months ago by tallnuttphone • 0

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540

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UniFrac in R with just the OTU table?

phylogeny R metagenomics unifrac written 18 months ago by David • 120

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1.0k

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How to avoid a phylogenetic bias testing a hypothesis on a big set of bacterial genomes

genome unifrac phylogenetics bacteria written 2.6 years ago by khorms • 30 • updated 2.6 years ago by abascalfederico • 1.0k

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Recent Replies

A: how many index has to be constructed by STAR for TE analysis by h.mon ♦ 20k
If your interest is TEs alones, you may index the genome with the repeats gtf. If you want to qua...
A: NCBI Entrez not returning the correct DNA sequence for all entries by piet • 1.5k
> dnahandle= Entrez.efetch(db = "nuccore", id=dnaacc,rettype="fasta",retmode="txt",seq_start=s...
A: GWAS IN PLINK - SIMPLE YET COMPLICATED by chrchang523 ♦ 4.0k
This is explained at the beginning of the documentation for [--pheno][1]: > **--pheno** cause...
C: Faster way to get sequences from large fasta files? by emilywynn6 • 0
I've tried this out on a small test file, and I think this strategy will work and be much faster....
C: GWAS IN PLINK - SIMPLE YET COMPLICATED by RamRS ♦ 18k
IIRC the phenotype file is just IID, FID and the phenotype column from the traditional PED format...
C: Can one use STAR (splice-aware) to align genomic DNA (non-spliced) by goodez • 280
Thank you. I'm assuming you mean check if I have spliced alignments? Because my reads are most de...
C: Can one use STAR (splice-aware) to align genomic DNA (non-spliced) by michael.ante • 2.7k
I'd check if you have spliced reads or not. In my experience, STAR aligns the reads correctly; ...
C: Faster way to get sequences from large fasta files? by mike-zx • 80
obviously to make the "file_with_headers_list" you would: cat fasta | grep \> > file_w...
A: Faster way to get sequences from large fasta files? by mike-zx • 80
if you only need all the sequences without headers you could: cat fasta | paste - - | cut -f...
A: R read.table() saying line does not have correct number of elements - when I che by Chirag Parsania • 1.1k
Tidy way library(tidyverse) dd <- read_delim("~/Downloads/first200.csv" , delim = "...
C: Can one use STAR (splice-aware) to align genomic DNA (non-spliced) by goodez • 280
What do you mean I shouldn't get spliced reads? I already have the reads, which come from DNA seq...
C: Faster way to get sequences from large fasta files? by michael.ante • 2.7k
Wouldn't STAR-Fusion or Tophat-Fusion give you the insight you need? With these tools, you'll d...

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