Questions tagged [metagenome]

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11 views

Is there a way to extract reads assigned to a particular taxonomic node from SRA data?

I've noticed that SRR submissions have an 'Analysis' section, where one can see what organisms are enriched in the sample; there is even a great graphic display that uses Krona to highlight what ...
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1answer
21 views

Metagenomic shotgun data with internal control

For 24 human stool samples I have metagenomic shotgun reads from an Illumina platform. The reads were filtered and mapped against a bacterial species library and specific maps to species were kept and ...
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38 views

Python module for fetching NCBI id for a list of species

I have a list of scientific names of species. Is there a python module that can fetch NCBI taxonomy IDs?
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How to apply RDP, Greengenes and other special taxonomies in Krona?

I used Kraken 2 to classify my 16S metagenomic data using both RDP and Greengenes database. As these are special databases the taxonomic ids assigned do not match with the NCBI taxonomic ids. I found ...
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23 views

Illumina 16S amplicon sequencing of healthy human cohort

I am looking for a 16S amplicon (ideally V3-V4) dataset from Illumina paired-end sequencing, which is similar to the healthy human cohort of the human microbiome project. I am primarily interested in ...
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15 views

How to build ML tree among OTUs and 16s sequence

I have OTUs sequence generated from 16s V4 clean reads, and want to build maximum likelhood tree with selcted taxonomy 16s refseq from Sliva database. ...
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1answer
73 views

Is there a way to assemble contigs starting from a specific sequence?

My work involves searching for marker genes/fragments in metagenomic databases (like the Sequence Read Archive). Once I find these sequences, I would like to know more about the neighboring genomic ...
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1answer
59 views

API/website for blasting peptide sequence against database of all plant proteomes

I would like to blast a peptide sequence against all available plant proteome databases, i.e. a blastp metaproteome analysis. What tools are available? Which ...
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1answer
57 views

How to query the Human Microbiome Project (HMP) to find all subjects with both 16s and WGS workups?

I am looking for a query to run on the HMP database that will return all subjects who have had BOTH 16s and whole genomes sequence (WGS) workups. I am currently using this query... ...
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1answer
95 views

Viral Metagenomics

I am analyzing viral metagenomics data (Illumina Miseq) for the first time. I have used Ray for de novo viral genome assembly before but I haven't done metagenomics analysis before. I know that ...
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2answers
63 views

What are Approximate Read Counts (Library Sizes) and Lengths (Insert Sizes) for Next-Generation DNA Sequencers?

I am performing a simulation study and am curious about the parameters of my simulated metagenome. What are the library and insert sizes of some of the most "used" sequencers. Mainly, I am ...
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1answer
102 views

Using large databases with BLAT

I'm a computer scientist working with biologists at a small school that doesn't have dedicated bioinformatics staff. I apologize if I use incorrect terminology since I have limited bioinformatics ...
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2answers
158 views

Transform traditional blast output to `--outfmt 6`

I already run a blastx of many metagenomic databases (raw illumina reads) against the nr database. However, I forgot to add the --outfmt 6 argument to the code and ...
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200 views

Microbial diversity analysis using whole-genome metagenomic data

I have data, obtained from a single metagenomic DNA sample, that consists of two MiSeq FASTQ files (R1 and R2) that I merged using PEAR. Now I want to estimate the abundances of the bacteria taxa to ...
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183 views

How do I efficiently perform a metagenome screen of “all” species?

I’ve got an RNA-seq dataset with a large proportion of environmental RNA “contamination”. BLASTing random reads reveals that much of the data comes from bacterial, plant and viral RNA. My target ...
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2answers
117 views

Workflow of metabarcoding analysis

For a diet analysis of an insect-eating animal, all species in a sample shall be identified. For this a sequencing of the metagenomic sample was done, where the COI/COX region was used as a barcode ...
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3answers
228 views

Pooling data in metagenome assembly

I have 12 human gut microbiome WGS Nextseq reads (151 bp paired end). What will be an effective strategy to assemble a metagenome? Let us say I have already filtered the fastq for quality, adapter ...
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2answers
4k views

How to use Python to count k-mers?

I have some FASTQ sequence files and a FASTA file for some regions I'm interested in. I would like: Build an index for the FASTA file Use the index to count number of k-mers occurred in my sequence ...
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1answer
50 views

What's the scaling for HOMER metagenes?

I'm trying to use HOMER to make a metagene profile over gene bodies using a bedgraph file I've generated. The problem is that every time I do, I get really weird scaling on the y-axis. I should be ...
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3answers
201 views

Accidental mapping of eukaryotic reads in a metagenomic dataset

This is a question from /u/wipeyourmit on reddit. The original post can be found here. If I have a metagenomic dataset that contains reads from both eukaryotes and prokaryotes and then I annotate ...
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192 views

Rapid metagenomics classifiers on long read data [closed]

I recently used the minION (Nanopore, 9.4 flow cell, RAD001 kit) to generate a metagenome out of environmental samples. Passed reads weren't brilliant (196, average 1,594bp lenght), but working with ...