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Showing top results for tag: metagenomics • reset
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Job: 2 PhD Scholarships in Bioinformatics in ancient sedimentary DNA and microbial DNA
metagenomics phd ancientdna sedadna ngs
2 days ago by Gabriel R. ★ 2.8k
1
vote
2
replies
101
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Taxonomy assignment of viral RNA
assembly taxa metagenomics
4 days ago by biobiu ▴ 120
2
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2
replies
131
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How does e value for diamond blastx affects the result
analysis metagenomics genomics data
10 days ago by saraswati.awasthi22 • 0
1
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4
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265
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BAM file's reference sequence IDs doesnt match contigs ID's
files metagenomics alignment bam binning
10 days ago by v.berriosfarias ▴ 10
0
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1
reply
104
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bbcms vs bbnorm when working with highly uneven coverage
BBTools Metagenomics Megahit Assembly BBNorm
updated 15 days ago by 99k • written 15 days ago by ▴ 150
0
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1
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123
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How do I determine antibiotic resistant gene from a metagenome
metagenomics genomics antibioticresistantgene
updated 15 days ago by ▴ 160 • written 16 days ago by • 0
4
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3
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373
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K-mer usage in metagenome assemblies
Assembly metagenomics k-mer
14 days ago by v.berriosfarias ▴ 10
3
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3
replies
342
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Downsampling fastq reads
next-gen metagenomics
updated 17 days ago by ▴ 280 • written 10 weeks ago by • 0
0
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3
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276
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antismash 5.0 (New region concept) - counting BGCs
antismash metagenomics
updated 26 days ago by ▴ 30 • written 6 months ago by ▴ 40
0
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2
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217
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How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
kegg database metagenomics module
updated 26 days ago by ★ 10k • written 26 days ago by ▴ 290
143
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34
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50k
views
31 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen tutorial Tutorial
updated 4 weeks ago by ▴ 120 • written 8.4 years ago by ★ 1.6k
0
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3
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111
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Split already joined and demultiplexed pair end sequences into separate FASTA files
metagenomics qiime
5 weeks ago by haig.they • 0
0
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0
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93
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News: Spring Bioinformatics Courses @ Edinburgh Genomics
RNA-Seq SNP metagenomics training News
5 weeks ago by Edinburgh Genomics Training ▴ 40
2
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4
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141
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LEfSe for multiple samples
RNA-Seq metagenomics environmental genomics
updated 6 weeks ago by 32k • written 6 weeks ago by ▴ 40
3
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6
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4.5k
views
How To Trim An Arb Reference Database To A Specific 16S Region
database trimming phylogenetics metagenomics
updated 7 weeks ago by • 0 • written 8.0 years ago by ▴ 150
0
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3
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159
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How can I run "gene set enrichment" (not necessarily GSEA) with only one condition?
metagenomics gene set enrichment analysis GSEA
7 weeks ago by O.rka ▴ 290
1
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3
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157
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How to run nucmer without reference? (viruses metagenomics)
assembly clustering metagenomics virus nucmer
updated 8 weeks ago by ★ 2.7k • written 8 weeks ago by ▴ 30
0
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0
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168
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Using different tools for different database sequences to identify antibiotic resistance genes.
NGS alignment metagenomics antibiotic resistance
8 weeks ago by dymphan.17phd • 0
0
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0
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149
views
What format are GTDB-Tk newick trees and how to extract specific node?
metagenomics gtdb database phylogeny
9 weeks ago by O.rka ▴ 290
1
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2
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510
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Better way for speedup of Humann3 metagenomics analysis pipeline?
alignment metagenomics humann pipeline
updated 9 weeks ago by ★ 1.4k • written 9 months ago by ▴ 120
0
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0
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124
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Including mock community in the Mothur MiSeq SOP pipeline
Mothur Metagenomics Mock-community 16s
10 weeks ago by spriyansh29 ▴ 30
8
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8
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1.6k
views
Taxonomic sequence classification for shotgun metagenomics, compatible with downstream statistical analyses
metagenomics shotgun sequencing Kraken2 phyloseq
updated 11 weeks ago by • 0 • written 17 months ago by ▴ 90
1
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1
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153
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alpha diversity metrics for relative frequency data
R metagenomics statistics
11 weeks ago by plicht • 0
0
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0
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150
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Which diversity index for relative abundance data?
Statistics R metagenomics OTU phyloseq
12 weeks ago by plicht • 0
3
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3
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3.0k
views
Enrichment Methods In Metagenomics
enrichment analysis metagenomics
updated 12 weeks ago by 20 • written 9.7 years ago by ▴ 110
0
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1
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153
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Why are there soo many hits when using KOFAMSCAN?
annotation protein metagenomics
updated 3 months ago by ★ 10k • written 3 months ago by ▴ 290
3
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0
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227
views
News: ONLINE TRAINING: Environmental Metagenomics
assembly metagenomics nanopore illumina News
3 months ago by carlopecoraro2 ★ 2.0k
0
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2
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537
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Is it normal that nearly all of p-value is equal to 0.1 in PERMANOVA analysis
PERMANOVA statistics metagenomics
updated 3 months ago by • 0 • written 15 months ago by ▴ 140
0
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2
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180
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Where can get processed metagenome datasets?
metagenomics sequencing meta-genome
3 months ago by m.koohi.m ▴ 120
0
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0
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204
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Combining prodigal for metagenomics and transdecoder for metatranscriptomics in same dataset?
metagenomics metatranscriptomics orf calling
4 months ago by O.rka ▴ 290
1
vote
1
reply
184
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Metagenomics - Functional analysis
metagenomics megan
4 months ago by lagartija ▴ 90
2
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3
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164
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Embedding Metagenomics Tools onto a Website
metagenomics bacteria fungi alignment sequencing
updated 4 months ago by 24k • written 4 months ago by • 0
0
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1
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172
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Can I use metatranscriptomic reads for coverage when doing metagenomic binning?
metagenomics metatranscriptomics binning
updated 4 months ago by ★ 10k • written 4 months ago by ▴ 290
3
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3
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390
views
Potential Bacteria Contamination - RNA-Seq
RNA-Seq metagenomics
updated 5 months ago by ▴ 130 • written 8 months ago by ★ 1.1k
0
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0
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190
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Remove certain species from standard database of Kraken
RNA-Seq 16s kraken bracken metagenomics
updated 5 months ago by 20 • written 5 months ago by ▴ 40
0
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4
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277
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Preparing 16S gene amplicon (metagenomic) sequencing data for submission to ENA
16S metagenomics sequencing ENA
updated 5 months ago by ★ 2.0k • written 5 months ago by • 0
3
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0
replies
433
views
Job: Associate Principal Investigator, Bioinformatics (1604)
next-generation sequencing metagenomics Job
5 months ago by tonya.stefanic ▴ 70
1
vote
3
replies
323
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viral metagenomics classification: MINIMUM number of viral reads (cutoff) to consider a sample positive
metagenomics classification ngs
6 months ago by Mania • 0
1
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3
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234
views
memory allocation in metaSpades
spades metagenomics RAM Assembly
updated 6 months ago by 99k • written 6 months ago by • 0
0
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0
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224
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Counting Biosyntheic Gene Clusters (BGC) types from Antismash Output
antismash metagenomics
6 months ago by arshad1292 ▴ 40
18
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5
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7.2k
views
Open Source Sequence Assembly Programs
metagenomics assembly open software
updated 6 months ago by 20 • written 10.3 years ago by ▴ 300
2
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4
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212
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mapping to incomplete reference
alignment mapping bowtie2 metagenomics
updated 6 months ago by 99k • written 6 months ago by • 0
0
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0
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257
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How to normalize between samples in WGS metagenomics
Metagenomics shotgun metagenomics Normalization
6 months ago by plicht • 0
0
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0
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217
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Performing so-called "SNP confirmation" for reads assigned to their corresponding Antibiotic Resistance Genes (ARGs): suggestions?
SNP ARG Reads Megares Metagenomics
updated 6 months ago by 20 • written 7 months ago by ★ 3.4k
1
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0
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399
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Job: PostDoc position at Human Genome Sequencing Center @ Baylor College of Medicine, Houston, TX, USA
job bioinformatics postdoc metagenomics Job
7 months ago by Medhat 8.9k
0
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10
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2.1k
views
Tools for metagenomics classification using long reads
metagenomics sequen alignment
updated 7 months ago by ▴ 30 • written 3.0 years ago by 8.9k
0
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6
replies
301
views
What are the input files for lwaldron / metaphlanToPhyloseq.R ?
r metagenomics metaphlan
updated 7 months ago by ▴ 250 • written 7 months ago by ▴ 40
1
vote
1
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398
views
Taxonomic classification of MAGs
metagenomics genome taxonomy binning
updated 8 months ago by ★ 10k • written 8 months ago by ▴ 40
2
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2
replies
258
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What does "assembly-level" classification mean?
classifier metagenomics classification
updated 8 months ago by 32k • written 8 months ago by • 0
1
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3
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282
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Good Books/Resources to learn metagenomic analysis?
metagenomics assembly bacteria nanopore long reads
updated 8 months ago by ★ 10k • written 8 months ago by ▴ 10
50 results • Page 1 of 1
Recent Votes
Comment: R command worked yesterday, but stalls today?
Answer: R command worked yesterday, but stalls today?
Comment: How to combine 2 incomplete GTF
Answer: comprehensive bacterial phylogenetic tree with edge lengths for all of RefSeq or
Comment: How can I Extract Transposable element from a new genome assembly?
Answer: How to combine 2 incomplete GTF
Answer: How to combine 2 incomplete GTF
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Popular Question to marongiu.luigi ▴ 560
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Recent Replies
Comment: how to select peaks at not transcribed genes by jared.andrews07 9.3k
In that case, wouldn't you consider all peaks to be associated with transcription? Even if your 232 peaks are not associated with genes, th…
Answer: Filter contig fasta file by GC content by GenoMax 99k
Try the following. seqkit fx2tab --name --only-id --gc contigs.fa | awk -F "\t" '{if ($2 < 35) print $1}' | xargs -n 1 sh -c 'seqki…
Comment: how to select peaks at not transcribed genes by Lila M ▴ 910
indeed, my IP was for Pol2
Comment: R command worked yesterday, but stalls today? by dariober 12k
...besides, [wget](https://www.gnu.org/software/wget/manual/wget.html) has a `-c/--continue` option to resume the download of a partial fil…
Comment: how to select peaks at not transcribed genes by jared.andrews07 9.3k
What makes you think genes with a peak are transcribed while those without are not? Unless your IP was for Pol2, this is an overly simplist…
Comment: How to combine 2 incomplete GTF by rafaelsolersanblas ▴ 70
Thank you! I am going to try it :)
Comment: How to combine 2 incomplete GTF by GenoMax 99k
Please create a new environment when installing packages. That avoids conflicts. conda create -c bioconda -n agat agat conda acti…
Comment: How to combine 2 incomplete GTF by rafaelsolersanblas ▴ 70
Hi Juke, I am trying to install it and I can't. ![enter image description here][1] [1]: /media/images/bc08978b-10f7-4666-b385-57807b…
Comment: comprehensive bacterial phylogenetic tree with edge lengths for all of RefSeq or by cmo ▴ 70
I agree with you, Mensur, that the GTDB is arguably more reliable and comprehensive than NCBI. However, due to the relative greater longevi…
Comment: how to select peaks at not transcribed genes by Lila M ▴ 910
rigth, it is a ChIP seq analysis
Comment: how to select peaks at not transcribed genes by ATpoint 48k
Which type data are we talking about? What was the experiment? There are literally no details in this question right now. It the assay meas…
Comment: How to combine 2 incomplete GTF by rafaelsolersanblas ▴ 70
Thank yo so much Juke!
Comment: MASURCA output by kilcdincer ▴ 10
Thank you. I understood ploidy part. My genome is supposed to belong to diploid Candida albicans. And genome size of diploid Candida alb…
Answer: How to combine 2 incomplete GTF by Juke34 ★ 5.3k
To give more precision to the @genomax comment: `agat_sp_compare_annotations.pl` will tell you the differences. Then you can choose to …
Comment: GSEA for RNA_seq dataset by ATpoint 48k
No problem. I am not really familiar with what the GSEA implementation from the Broad institute does. I personally use fgsea from Bioconduc…
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