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Showing top results for tag: metagenomics • reset
2
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How do you split metagenomic bins/MAGs into eukaryotic and prokaryotic?
protist metagenomics prokaryotic eukaryotic gtdbtk
updated 1 day ago by ★ 12k • written 1 day ago by ▴ 320
7
votes
4
replies
269
views
Difference between a bin and a MAG
metagenomics mags binning
2 days ago by Maria Laura • 0
0
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0
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47
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using a singualrity application ARGs-OAP
Data-Analysis WholeShotgunMetagenome AMR Microbiome Metagenomics
3 days ago by saraswati.awasthi22 • 0
3
votes
4
replies
176
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Removal of host reads from shotgun metagenomics data.
metagenomics shotgun
updated 4 days ago by 104k • written 4 days ago by • 0
2
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0
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73
views
Tool: metaGEM: create your own genome scale metabolic models directly from metagenomes
metagenomics metagenome-assembled-genome genome-scale-metabolic-model metabolism
updated 11 days ago by 34k • written 11 days ago by ▴ 20
0
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0
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61
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hclust2.py heatmap in MetaPhlAn3 --ftop features
MetaPhlAn3 Data-Analysis WholeShotgunMetagenome Microbiome Metagenomics
11 days ago by saraswati.awasthi22 • 0
0
votes
3
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188
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Several contigs hit the same species with viralComplete : which contigs should I use to map the reads with bowtie2?
contigs bowtie2 viralComplete metagenomics
updated 12 days ago by ★ 1.6k • written 12 days ago by • 0
0
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0
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120
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What are the minimal contig length and kmer coverage below which I should drop some contigs in viral metagenomics study after assembly with Spades?
Kmer Length Contigs coverage Metagenomics
11 days ago by bioAddict • 0
0
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0
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68
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How to make a genomic content table that has species as the rows and functions (pathways or genes) on the column?
metagenomics
14 days ago by dpc ▴ 190
0
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0
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106
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High Number of Unassigned Reads in MEGAN?
diamond megan metagenomics
19 days ago by ian.petersen • 0
2
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2
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155
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How Should I Deal with Paired-End Shotgun Metagenomic Reads for DIAMOND Analysis?
diamond metagenomics megan paired-end
updated 20 days ago by 33k • written 20 days ago by • 0
0
votes
1
reply
97
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Rarefy metagenomic adatasets for taxonomic profiling using MetaPhlAn3
metagenomics Rarefy MetaPhaln3 Genomics
updated 25 days ago by ★ 1.6k • written 25 days ago by • 0
0
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0
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144
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Job: Bioinformatics Scientist openings in Central Florida
metagenomics metabolomics scRNAseq proteomics DNAseq
27 days ago by qysl • 0
0
votes
1
reply
117
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Adding insect abundance data to SparCC Analysis
Microbiome metagenomics 16S microbiome SparCC
updated 29 days ago by 75k • written 29 days ago by ▴ 10
2
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3
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193
views
Assembly of three biological replicated metagenomics data
Assembly metagenomics analysis replicate statistics
updated 4 weeks ago by ★ 1.6k • written 4 weeks ago by • 0
0
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7
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462
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What are the input files for lwaldron / metaphlanToPhyloseq.R ?
r metagenomics metaphlan
updated 4 weeks ago by • 0 • written 11 months ago by ▴ 40
0
votes
1
reply
123
views
import metaphlan3 output to Phyloseq
Phyloseq metagenomics MetaPhaln3 Genomics
updated 4 weeks ago by ★ 2.1k • written 5 weeks ago by • 0
1
vote
0
replies
77
views
Pattern Search function in MicrobiomeAnalyst
MicrobiomeAnalyst metagenomics
5 weeks ago by GlycineMax ▴ 10
1
vote
3
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287
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Job: Bioinformaticist or computational biologist opportunity at Pattern Ag (CA, USA) in metagenomics
metagenomics python development NGS
updated 4 weeks ago by 34k • written 5 weeks ago by • 0
4
votes
3
replies
203
views
high duplication events in shotgun metagenomics
MAG metagenomics duplication
5 weeks ago by alexis ▴ 10
2
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4
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214
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Viral metagenomics of RNA virus on transcriptomics data workflow
Viral metagenomics workflow
5 weeks ago by bioAddict • 0
1
vote
2
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146
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FastQC report of the metagenomic data
Metagenomics Microbiome WholeShotgunMetagenome FastQC Data-Analysis
6 weeks ago by saraswati.awasthi22 • 0
1
vote
4
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215
views
Subsampling reads
metagenome metagenomics microbial
7 weeks ago by Elaine • 0
0
votes
0
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91
views
How to fix "Please indicate the file directory in 'setting' file?" for MaxBin2?
binning maxbin2 error metagenomics
7 weeks ago by O.rka ▴ 320
1
vote
0
replies
78
views
Discussion on binning multiple metagenomes at the same time?
binning metagenomics mags
7 weeks ago by O.rka ▴ 320
0
votes
0
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117
views
How to use transcript coverage for ORF calls on contig?
gene-calling virus metatranscriptomics metagenomics
8 weeks ago by O.rka ▴ 320
0
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3
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184
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top 25 species from all sample datasets
Metagenomics Data-Analysis WholeShotgunMetagenome Microbiome
updated 8 weeks ago by ▴ 880 • written 8 weeks ago by • 0
1
vote
1
reply
147
views
MEGAN6 Ultimate Edition
Metagenomics MEGAN6
updated 8 weeks ago by 20 • written 8 weeks ago by • 0
0
votes
1
reply
151
views
Bracken tool - do genus abundances need to be analysed on genus level or species/strain level?
kraken microbiome levels metagenomics bracken
updated 9 weeks ago by ★ 3.0k • written 9 weeks ago by ▴ 10
1
vote
1
reply
166
views
Best method to visualize metagenomic data besides krona?
metagenomics krona
updated 9 weeks ago by ★ 1.6k • written 9 weeks ago by ▴ 180
0
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0
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90
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Fatal error: exit code 1 () using make.shared
galaxy metadata metagenomics mothur error
11 weeks ago by elfellah.aymane00 • 0
1
vote
5
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277
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Using np to target subsampling
nonpareil coassembly metagenomics
updated 11 weeks ago by 33k • written 11 weeks ago by ▴ 10
0
votes
1
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494
views
Job: Multiple Opportunities in Microbial Computational Biology at Lanzatech
Sequence_Analsyis Metagenomics Modeling AI Systems
updated 11 weeks ago by 16k • written 11 weeks ago by • 0
0
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0
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122
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Metaquast largest contig by species identical for most species in the metagenomic assembly
metagenomics species quast contig metaquast
12 weeks ago by Macspider ★ 3.4k
0
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0
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79
views
Whole Metagenome Analysis of resistome dataset
metagenomics ngs
3 months ago by hafiz.talhamalik ▴ 310
4
votes
3
replies
327
views
Normalize by contig size BEFORE RPKM normalization?
virus normalization metagenomics edgeR RPKM
updated 12 weeks ago by ★ 2.6k • written 3 months ago by ▴ 150
1
vote
0
replies
290
views
Job: 2 PhD Scholarships in Bioinformatics in ancient sedimentary DNA and microbial DNA
metagenomics phd ancientdna sedadna ngs
3 months ago by Gabriel R. ★ 2.8k
1
vote
2
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271
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Taxonomy assignment of viral RNA
assembly taxa metagenomics
3 months ago by biobiu ▴ 120
2
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2
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307
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How does e value for diamond blastx affects the result
analysis metagenomics genomics data
3 months ago by saraswati.awasthi22 • 0
1
vote
4
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458
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BAM file's reference sequence IDs doesnt match contigs ID's
files metagenomics alignment bam binning
3 months ago by v.berriosfarias ▴ 30
0
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1
reply
228
views
bbcms vs bbnorm when working with highly uneven coverage
BBTools Metagenomics Megahit Assembly BBNorm
updated 3 months ago by 104k • written 3 months ago by ▴ 150
0
votes
1
reply
206
views
How do I determine antibiotic resistant gene from a metagenome
metagenomics genomics antibioticresistantgene
updated 3 months ago by ▴ 400 • written 3 months ago by • 0
4
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3
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495
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K-mer usage in metagenome assemblies
Assembly metagenomics k-mer
3 months ago by v.berriosfarias ▴ 30
3
votes
3
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577
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Downsampling fastq reads
next-gen metagenomics
updated 4 months ago by ▴ 280 • written 5 months ago by • 0
0
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3
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438
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antismash 5.0 (New region concept) - counting BGCs
antismash metagenomics
updated 4 months ago by ▴ 80 • written 9 months ago by ▴ 40
0
votes
2
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336
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
kegg database metagenomics module
updated 4 months ago by ★ 12k • written 4 months ago by ▴ 320
145
votes
34
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51k
views
31 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen tutorial Tutorial
updated 4 months ago by ▴ 120 • written 8.7 years ago by ★ 1.6k
0
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3
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218
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Split already joined and demultiplexed pair end sequences into separate FASTA files
metagenomics qiime
4 months ago by haig.they • 0
0
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0
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172
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News: Spring Bioinformatics Courses @ Edinburgh Genomics
RNA-Seq SNP metagenomics training News
4 months ago by Edinburgh Genomics Training ▴ 40
2
votes
4
replies
358
views
LEfSe for multiple samples
RNA-Seq metagenomics environmental genomics
updated 4 months ago by 33k • written 4 months ago by ▴ 40
50 results • Page 1 of 1
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A: Identifying discordantly mapped reads
RNA-seq: Explain STAR quantMode geneCounts values
Comment: plant viruses sequences
Trinity strand specific: RF or FR
MSMC: very high Ne close to present
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to filter VEP results of "missing values"
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Recent Replies
Comment: How to extract sample id using bcftools or vcftools by Ömer An ▴ 230
You can refer [here][1]. [1]: http://manpages.ubuntu.com/manpages/impish/man1/vcf-query.1.html
Answer: How to find the names of elements while parsing PDB files via biopython? by Tzunami • 0
Found the solution (atom entries have an attribute called element which returns the element of the corresponding atom) - for model …
Comment: plant viruses sequences by Ric ▴ 350
Thank you, I click the Download bottom from your first link, selected land plants and downloaded the following files: ``` $ ls -hlatr total…
Comment: plant viruses sequences by GenoMax 104k
[**Viral genomes browser**][1] is available from NCBI. Use `filter by host` (land plants seems to generate plenty of results). There is a `…
Comment: inquiry related to snpsift by Kevin Blighe 75k
As with many things in bioinformatics, the VCF specification has been misused over the years. Take into account, also, that different progr…
Comment: gene expression of specifics gene by Bioinformatics1 • 0
I have log2(Fold Change) for two groups. Is there any instruction/pipelines I can use for gene expression using log2(Fold Change) in R? M…
Answer: use a list of id to extract sequence from different genomics by Pierre Lindenbaum 137k
[linearize][1] and extract the ID at the same time, sort both list, join, restore the fasta: join -t $'\t' -1 1 -2 1 \ <…
Comment: use a list of id to extract sequence from different genomics by LZH289 • 0
thank you!
Comment: What does betaPrior do in DESEQ? by i.sudbery 12k
Those DE genes - is that after a log fold change cut off?
Answer: How to filter VEP results of "missing values" by Yiming ▴ 10
Thank you so much! I found an error with my code. And this works: filter_vep -i VEP_annotated.vcf -o VEP_filtered.vcf --format vcf …
Comment: use a list of id to extract sequence from different genomics by GenoMax 104k
Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time. <br /> <img src="…
Comment: gnomaAD exome and genome AF differences by humzakhan340 • 0
The point that genomes are much larger and more computationally intensive to work with is well-taken. However, promoter information is not…
Comment: ERROR [mem_sam_pe] paired reads have different names -- during binning in metaW by swbarnes2 10k
Do you understand what the problem is? Have you figured out which step introduced it?
Comment: gene expression of specifics gene by Bioinformatics1 • 0
Thanks Hyper-Odin
Comment: inquiry related to snpsift by rheab1230 • 0
I have one question related to earlier step where you are formating the .vcf file. You are removing white space and removing format tags ex…
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