Hi
I am new to metagenomics data analysis.
Currently I am working on nifH amplicon data.
I have done quality filtering, reads merging,...
19 results in 0.0023 seconds.
-
How to use ARB nifH database(Zehr et. al) for taxonomic assignment
Hello members,
I am new in metagenomics data analysis. Currently I am working on a nifH amplicon data. I have done quality filtering, merging and... -
Pfam search using hmmer but only for a specific taxonomy
I am trying to do a de novo assembly using Trinity. Using Transdecoder and blastp/hmmscan search to do annotation (using Uniprot/pfam databases). htt... -
Profiling taxonomic distribution of genes in human gut microbiome
Dear Seqanswers community,
I am trying to determine the abundance and taxonomic distribution of a gene cluster in human gut microbiome... -
BLAST taxid to complete linage using biopython on a local machine.
Hello all,
Using BLAST, I am trying to identify thousands of sequences. To make my job a bit easier, I would like to classify these sequences... -
Generate local blast database with RefSeq bacteria AND taxonomy
Dear all,
I would like to be able to create my own custom local blast database, as this may be relevant in many different situations in... -
raw illumina reads or assembled contigs for Taxonomy
Hello!
I am having whole genome sequenced metagenomic data that is assembled using meta-velevt. I want to check taxonomic classification... -
PCoA Plots
Hi Everyone,
I have HiSequencing data that I want to set up PCoA plots for.
These are environmental samples and I want to look at the diversity... -
MinHash Sketch - A Tool for Rapid Sequence Comparison
MinHash Sketch is a method of rapidly comparing large strings or sets. In genomics, you can use it like this:
1) Gather all the kmers...Last edited by Brian Bushnell; 02-03-2017, 08:53 AM. -
Using DeSeq2 in R or Qiime to examine taxonomic rank other than OTU level
Hello,
I am trying to follow the example given here https://github.com/joey711/phyloseq/issues/683, using DeSeq2 to examine differential... -
RDP: what does (T) mean in sequence identifier?
Hi There,
I'm downloading sequences from RDP for genera, and species I'm interested in. Upon downloading I see few sequence identifiers have (T)...Last edited by bio_informatics; 08-02-2016, 06:10 AM. -
RDP classifier - training set: how do I create?
Hi there,
I've nasal and genital microbiome: 16S rRNA, Illumina 300BP, paired end data. For various reasons green-genes, and silva database... -
What's the best way to identify the taxonomy of assembled genomes?
Hi everyone,
Briefly, I applied coverage-based binning method plus pentamer-frequency ordination on metagenomic assembled contigs, to isolate individual... -
Identifying a draft genome
Hi everyone,
I have a draft genome which was binned from a bacterial metagenome. I know for certain that the genome doesn't have a 16s gene in... -
Qiime parallel_pick_otus_uclust_ref.py
Good morning everyone!
I ran parallel_pick_otus_uclust_ref.py with a high quality fasta file and silva.nr.v119.align as the refence file....
