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63,785 results • Page 1 of 1276

Hi, I am new to shotgun metagenomics. Currently, I got some data from shotgun metagenomics. And now I just want to know the general taxonomy...of my data. Since then I can compare it with my 16S amplicon result to check the bias of the 16S data. Is there any clue to doing this? Thanks

sequencing

updated 6.1 years ago • luyang1005

I want to compare two genomes that I obtained from my shotgun metagenomic sequencing data. Seems like "cd-hit-est-2d" option works perfectly for me as I need to find out what sequences...these two genomes. However, I read in the CD-HIT manual that it's good for non-intron containing sequences e.g. EST. That means I SHOULD NOT use CD-HIT for my metagenome comparison? If not, please suggest any ot…

shotgun CD-HIT metagenome genome

updated 2.3 years ago • arshad1292

I am looking at some shotgun (not amplicon) metagenomics data, and have observed that among the reads that are classified as belonging to specific...in the classification results because those portions of the genomes are "close enough" to previously sequenced genomes. My first question is: is this a plausible interpretation of what I'm observing? Follow-up: is it a common issue...with shotgun me…

metagenomics sequencing microbiome

updated 6.3 years ago • grp2009

The presence of host sequence in shotgun metagenome data is considered as contamination and it is removed by mapping with a reference genome...Can anyone kindly through some light on how to create the reference genome when the whole genome sequence data is not available for the host organism? I am currently working on the gut microbiota of a lepidopteran species...and its whole genome is not sequ…

metagenomics shotgun

updated 2.8 years ago • dharitrisaikia162

Hello! I have 9 environmental shotgun metagenomics libraries where the data were assemble (with Ray software) and the protein-coding genes sequences predicted...with Glimmer by the bioinformaticians from the sequencing company. Now, I would like to predict the function of the protein-coding genes in fasta format from the 9 metagenomics...row) within each sample. My question is: Which soft…

next-gen sequencing gene

updated 7.2 years ago • antonioggsousa

Hello, I have a whole metagenome shotgun data processed by trimmomatic, metaspades and bowtie. Please tell me what to do next? It is necessary to

metagenome genome

updated 3.2 years ago • kocharovskayaj

Hi, I'd like to test my metagenomic pipeline with an ATCC positive control. I know there's CAMISIM and WGSIM which can simulate shotgun metagenomics...reads but I'd like to know if there is a database of real Illumina paired-end positive control sequence data

shotgun metagenomic

updated 4.7 years ago • BioinformaticsLad

We have done a large scale shotgun metagenome over 100 samples and analysed using metaphlan2. Can anybody help me out how to perform a Rarefaction analysis...In case of amplicon we can subsample the reads and perform the analysis but what should we do in shotgun metagenome sequencing

sequence metagenome

updated 4.3 years ago • jeccy.J

Hi all, So, I'm new in shotgun metagenomic analysis and I have a doubt... I have some raw sequences data, with four files per experimental group, e.g...bigger in size than _L3_... But the question is: what should I consider in my analysis? Only _L1_ sequences? Both? Thank you in advance

metagenomics shotgun metagenomic

updated 18 months ago • vini.drr

Hi everyone, I am seeking some info related to shotgun metagenomic data analysis. I am a beginner in metagenome analysis. Recently we did a shotgun metagenome sequencing...for few of my samples. we did through Iontorrent sequencing. I want to extract only 16S rRNA gene sequences from metagenome to compare with my amplicon sequencing data. Does

next-gen genome Assembly sequencing

updated 6.8 years ago • venkateshbiotech

hello everybody! I would ask you about the tools that I can use for analyse the data of shotgun metagenomic, and also i would if we can use the tools that we use for analyse the 16 RNA amplicon like : Mothur or

next-gen genome

updated 5.1 years ago • haddadfatiha62

Hi Everyone!! Is it possible to detect RNA viruses from shotgun metagenomics data except for the retroviruses? I am curious because we have found retroviruses from our shotgun...metagenome data but that is explainable because the retroviruses have the machinery to integrate into the DNA (genome) and...replicate so they can be detected but other RNA viruses can't be detected from the shotgun meta…

genomics Metagenomics Microbial Viruses RNA-Viruses

updated 12 months ago • serene.s

on understanding the relation between gut microbiome and cognition. We would like to perform shotgun metagenomics analysis. I am a bit sceptical about the availability of bacterial reference database. Could you please...let me know 1) Which is the best reference database for bacterial metagenomics. 2) What is the workflow for shotgun metagenomics. Thank you

sequencing next-gen Assembly

updated 5.5 years ago • mrudhulaks

Is there any tool to extract a specific strain genome from mouse gut microbiome shotgun metagenome sequence

genome

updated 7.0 years ago • lxu12

that would suit my needs. Hence, I would kindly ask for your opinion and advice. I have Illumina shotgun sequences of 5 metagenomes. I would like to end up with functional profile of all 5 samples that can be comparable. In

metagenomics workflow shotgun

updated 7.5 years ago • deni.ribicic

Hi all, I would like to align the shotgun metagenomics data to a set of protein sequences of interest to estimate their abundance in the metagenome. I found

reference protein metagenome database paladin

updated 12 months ago • zhangdengwei

Hello Biostars, I've been given occasion to plunge into the metagenomics field. I'm working with **shotgun** sequencing data, so not targeted at 16S or another gene. From reading several articles...review by Siegwald *et al.*][1], and the websites of QIIME and mothur, it seems that targeted (non-shotgun) analyses are the standard, but that I cannot use the same software to analyse shotgun sequen…

metagenomics shotgun sequencing Kraken2 phyloseq

updated 3.3 years ago • DriesB

Dear all, I am new to metagenomics. My question might seem to be naive. As the title implies, how different are the species abundance simply using...16S rRNA data in 16S rRNA amplicon sequencing data and shotgun metagenome data (by selecting 16S rRNA reads) based on current technology...I came across one paper titled "[Comparing bacterial communities inferred from 16S rRNA gene sequencing and sh…

metagenomics species-profiling

updated 18 months ago • concer.guo

Hi, I have some shotgun metagenomics gonorrhea samples and I want to use metagenomics pipeline to process the samples and then detect antimicrobial...resistance. I looked into few pipelines so far for metagenomics data such as ATLAS, Sunbeam, MetaSUB/CAP2 and nf-core/mag. They have different steps of data processing with different

metagenomics_pipelines WGS shotgun_metagenomics antimicrobial_resistance

updated 2.7 years ago • eli_bayat

Are there any raw data available for whole genome shotgun of soil metagenomes? There are a few studies here and there, but these are mostly 16S...Are there any raw data available for whole genome shotgun of soil metagenomes? There are a few studies here and there, but these are mostly 16S rRNA studies, not full sequencing. I know MGRAST contains a few studies and I stumbled across Terragenome i…

metagenomics next-gen

updated 7.1 years ago • Pawel Szczesny

Hi all, I am working on a project that aims to recover Metagenome assembled genomes using shotgun metagenomics. During the quality analysis using FastQC I found high duplication...levels (percent of sequences remaining if deduplicated is 27%). However, from previous amplicon metagenomics, I know that I am working with a low

MAG metagenomics duplication

updated 2.9 years ago • alexis

Hi, I am new to shotgun metagenomics analysis. However, I have used Metaphlan2, kraken, minikraken to try on my samples. The results are totally

next-gen sequencing

updated 5.9 years ago • luyang1005

Hi, I am working on sewage and river water sample metagenome analysis. With the shotgun metagenome approach, we can obtain genomes of bacterial and archaeal groups. Is it possible...to capture the complete genome sequences of RNA viruses specifically? In some cases, the viral load is extremely low in water samples. Is there any way to target...both RNA and DNA viruses using the shotgun metagenome…

RNA-virus binning metagenome abundance shotgun

updated 7 weeks ago • mathavanbioinfo

Hi.... I have analysed my shotgun data with MetaPhlAn 3.0. Now I want to do statistical analysis of my output data. Is it possible to analyse my data with...the curated metagenomic data pipeline? Or, is this pipeline for submitted datasets only? Thanks, DPC

metaphlan curated metagenomic data

updated 3.8 years ago • dpc

Hello. I have shotgun sequencing data. I have a list of bacteria at the species level and a list of genes. What R package do you usually use to

deg degs shotgun

updated 11 weeks ago • sooni

I have several shotgun metagenome datasets. I'm interested in one strain and would like to pick the reads fro that strain from metagenome

metagenome

updated 6.0 years ago • xuling2015

Hello, I have obtained two files through illumina shotgun sequencing forward and reversde and would like to perform assembly of my metadata. kindly suggest an easy to use metagenomic

Assembly genome next-gen sequencing

updated 7.4 years ago • faizansaleem1992

Hello. I have 4 shotgun sequencing data of soil microbial communities. I have compiled a custom database of genes of polyciclic aromatics...catabolism and mapped my raw shotgun reads to this database. So from each sample I obtained reads corresponding to PAH catabolic genes. For example: sample

shotgun metagenome

updated 3.1 years ago • mewgia

Hi. I'm wanting to reconstruct gene from shotgun metagenome reads, ***but using only a specific read***. Anyone know a good analysis tool for it? Best Y.A.T

Shotgun Gene Metagenomics

updated 2.2 years ago • Y.A.T.

Hi there community! For some time I was working os 16S rRNA gene survey data. For this type of analysis one could use a rarefaction approach in order to have the same depth for each sample. Having...Hi there community! For some time I was working os 16S rRNA gene survey data. For this type of analysis one could use a rarefaction approach in order to have the same depth for each sample. Having d…

metagenomics whole genome sequencing shotgun

updated 4.3 years ago • robert.kwapich

assessing bacterial diversity and detecting the abundance of microbes in various environments from **shotgun** metagenomic sequencing data. I hope you can help me with the pipeline, tools, and databases that we can use in this case

shutgun metagenomics

updated 6 months ago • scarlettpigany

Hello! I'm very new to bioinformatics and metagenomics so apologies in advance if this is a very basic question. I'm trying to run a metagenomic analysis on a specific...a specific gene/protein in the species in the metagenome, my query sequences are in amino acid FASTA format while all the shotgun datasets are in nucleotides. While running...the tBLASTn query, all the results are just more sho…

metagenomics BLAST shotgun sequencing

updated 2.8 years ago • nojerama

Hello to everyone! I have 7 different metagenome datasets. I have to build a machine learning model using these datasets. This is my question; I want to bring together...7 different datasets into one huge data for the input of the model. Is it a data fusion or a data integration that brings all datasets together? According to my google...searches, both are different techniques. Ps. 2 of all met…

fusion data-integration metagenome

updated 22 months ago • seda

Hello, I am working on a shotgun metagenomics data. Briefly, after contig assembly, the ORFs were predicted usinf Prodigal, and annotations were carried

normalization metagenomics shotgun

updated 20 months ago • Eray Sahin

Hello dear all. My question is for people experienced in metagenomic analysis of complex microbial communities such as in soil. Suppose I have several soil shotgun metagenomes...and I need to classify all of it reaching maximum possible diversity stored in my data. As far as I know, current full-genome databases can be divided into curated (i.e. RefSeq, progenomes) and non-curated (i.e...ones. Us…

metagenomics shotgun annotation RDP biodiversity

updated 15 months ago • Konstantin

diagnostics lab. Since assembly-dependent methods are time-costly, we are looking for tools to give metagenomics the possibility to serve as diagnostic method. Thanks, Bernardo An example of these kind of tools is this one...Koslicki, David, Simon Foucart, and Gail Rosen. "WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification." *PloS one* 9.3 (2014): e91784

metagenomics

updated 2.2 years ago • biotech

I have few shotgun metagenomics samples. There is one of them when analyze it alone I get 300,000 hits against Refseq But when upload other

sequencing next-gen

updated 3.5 years ago • firminlago

I have some metagenomic shotgun sequencing data that is paired-end. I am considering using metaphlan2 and the biobakery workflows for...analysis. However, the documentation states that they recommend merging the paired-end sequencing data into one before beginning the analysis. My question is: 1.) Should I merge the sequencing data and the trim them

sequencing

updated 4.6 years ago • gtasource

Hi everyone, I've started learning about shotgun metagenomics sequencing. My understanding is there are two main approaches: mapping-based and assembly-based. In...species is not in the database, you wouldn't know what it is anyways. However, you could compare the sequences to see what it's similar to - but you can do that using the unassembled reads anyways. So given the large computational...…

metagnomics assembly

updated 5.3 years ago • BioinformaticsLad

bacterial diversity and detection of the abundance of microbes in various environments from Shotgun metagenomic sequencing data. I count on you expertise to guide me and give me what pipeline/ tools / databases we should

shutgun metagenomics

updated 6 months ago • scarlettpigany

I'm planning my first metagenomic experiment and hope to get some advice/comments before I start working on it. We are trying to explore the antimicrobial...of a plant and the idea here is to investigate the "killing effect" of the plant on the oral metagenomes. We are going to do shotgun metagenomes at 3 different time points after eating the plant. Initially we were thinking...of depleting the…

illumina metagenomics microbiome

updated 19 months ago • ivpz

For WGS sequencing, the DNA was sheared first and then cloned into a vector, finally assembly contig and PCR gaps. 1. I found clone is...For WGS sequencing, the DNA was sheared first and then cloned into a vector, finally assembly contig and PCR gaps. 1. I found clone is used...in shotgun method. So cloned based sequencing method is a part of shotgun sequencing or a separate method? Are they su…

sanger-sequencing

updated 12 months ago • mm521

Hello, I have some shotgun metagenomics data (long reads sequenced by ONT). I want to use those metagenomics data in order to detect the presence

metagenomics genes

updated 11 months ago • aziznasr1920

Hello! I have 4 samples of whole metagenome shotgun sequencing results (soil communities). Illumina, single end, read length ~76 bp. The raw reads were preprocessed

whole metagenome shotgun sequencing illumina

updated 3.2 years ago • mewgia

Hi all, I am currently performing blast searches for a species of interest by blasting a genome assembly against custom databases of metagenome shotgun data. Everything seems to be working fine and I am getting hits, if I create a database from a single sample (i.e. paired reads, converted fastq to fasta). But, as soon as I create a custom database from multiple samples, I am only getting hits …

metagenomics blast

updated 5.3 years ago • christina

Hello all, I have a shotgun metagenomic dataset (20 samples) paired-end reads. I want to compare my data to another dataset published and available

metagenomics

updated 15 months ago • arshad1292

I have large shotgun metagenomics assembled sample. Produced by RNA-Seq and assembled with Trinity software. I would like to put it in MG...I have large shotgun metagenomics assembled sample. Produced by RNA-Seq and assembled with Trinity software. I would like to put it in MG-RAST to study its taxonomic composition. As MG-RAST doesn't work well with eukaryotic sequences, which computational tool…

sequences eukaryotic shotgun-metagenomics MG-RAST

updated 19 months ago • BioNtE

Hello everyone. I was trying to run my raw data from shotgun sequencing through DADA2 and could not find a reference database for the simultaneous taxonomic assignment

dada2 shotgun assignment rawdata sequencing taxonomic

updated 17 months ago • Muhammad

Hi, community, I am analyzing the taxonomic profiling of my shotgun data. Which are 100bp paired-end reads from Illumina Hiseq. Now I am using Metaphlan2 to do the metagenomics profiling...16S reads tell me that only around 15% archaea and 85% bacteria for control samples. For treatment, shotgun profiling told me 60% archaea and 40% bacteria, while Miseq gave me 20% archaea and 80% bacteria. For…

sequencing

updated 6.1 years ago • luyang1005

Hi all, I was wondering if there was anyone on here that could tutor in metagenomics data processing? I am very new to the field, and I am trying to understand the basics of quality filtering, predicting...protein sequences, creating contigs and sequence binning. I am starting from raw reads from a soil microbial sample whole shotgun...sequencing experiment. If available and interested please…

metagenomics microbial tutoring

updated 11 months ago • MK2000

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