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Showing top results for tag:
metagenomics
•
reset
1
vote
0
replies
69
views
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
views
Taxonomy assignment of viral RNA
assembly
taxa
metagenomics
4 days ago by
biobiu
▴ 120
2
votes
2
replies
131
views
How does e value for diamond blastx affects the result
analysis
metagenomics
genomics
data
10 days ago by
saraswati.awasthi22
• 0
1
vote
4
replies
265
views
BAM file's reference sequence IDs doesnt match contigs ID's
files
metagenomics
alignment
bam
binning
10 days ago by
v.berriosfarias
▴ 10
0
votes
1
reply
104
views
bbcms vs bbnorm when working with highly uneven coverage
BBTools
Metagenomics
Megahit
Assembly
BBNorm
updated 15 days ago by
GenoMax
99k • written 15 days ago by
samlambrechts299
▴ 150
0
votes
1
reply
123
views
How do I determine antibiotic resistant gene from a metagenome
metagenomics
genomics
antibioticresistantgene
updated 15 days ago by
Shaminur
▴ 160 • written 16 days ago by
Himu22
• 0
4
votes
3
replies
373
views
K-mer usage in metagenome assemblies
Assembly
metagenomics
k-mer
14 days ago by
v.berriosfarias
▴ 10
3
votes
3
replies
342
views
Downsampling fastq reads
next-gen
metagenomics
updated 17 days ago by
onestop_data
▴ 280 • written 10 weeks ago by
plicht
• 0
0
votes
3
replies
276
views
antismash 5.0 (New region concept) - counting BGCs
antismash
metagenomics
updated 26 days ago by
timothy.kirkwood
▴ 30 • written 6 months ago by
arshad1292
▴ 40
0
votes
2
replies
217
views
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
Mensur Dlakic
★ 10k • written 26 days ago by
O.rka
▴ 290
143
votes
34
replies
50k
views
31 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
tutorial
Tutorial
updated 4 weeks ago by
juanjo75es
▴ 120 • written 8.4 years ago by
vijay
★ 1.6k
0
votes
3
replies
111
views
Split already joined and demultiplexed pair end sequences into separate FASTA files
metagenomics
qiime
5 weeks ago by
haig.they
• 0
0
votes
0
replies
93
views
News:
Spring Bioinformatics Courses @ Edinburgh Genomics
RNA-Seq
SNP
metagenomics
training
News
5 weeks ago by
Edinburgh Genomics Training
▴ 40
2
votes
4
replies
141
views
LEfSe for multiple samples
RNA-Seq
metagenomics
environmental genomics
updated 6 weeks ago by
h.mon
32k • written 6 weeks ago by
willnotburn
▴ 40
3
votes
6
replies
4.5k
views
How To Trim An Arb Reference Database To A Specific 16S Region
database
trimming
phylogenetics
metagenomics
updated 7 weeks ago by
1731147b
• 0 • written 8.0 years ago by
samlambrechts299
▴ 150
0
votes
3
replies
159
views
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
vote
3
replies
157
views
How to run nucmer without reference? (viruses metagenomics)
assembly
clustering
metagenomics
virus
nucmer
updated 8 weeks ago by
colindaven
★ 2.7k • written 8 weeks ago by
Arsenal
▴ 30
0
votes
0
replies
168
views
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
votes
0
replies
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
vote
2
replies
510
views
Better way for speedup of Humann3 metagenomics analysis pipeline?
alignment
metagenomics
humann
pipeline
updated 9 weeks ago by
Raygozak
★ 1.4k • written 9 months ago by
boaty
▴ 120
0
votes
0
replies
124
views
Including mock community in the Mothur MiSeq SOP pipeline
Mothur
Metagenomics
Mock-community
16s
10 weeks ago by
spriyansh29
▴ 30
8
votes
8
replies
1.6k
views
Taxonomic sequence classification for shotgun metagenomics, compatible with downstream statistical analyses
metagenomics
shotgun sequencing
Kraken2
phyloseq
updated 11 weeks ago by
obriek11
• 0 • written 17 months ago by
DriesB
▴ 90
1
vote
1
reply
153
views
alpha diversity metrics for relative frequency data
R
metagenomics
statistics
11 weeks ago by
plicht
• 0
0
votes
0
replies
150
views
Which diversity index for relative abundance data?
Statistics
R
metagenomics
OTU
phyloseq
12 weeks ago by
plicht
• 0
3
votes
3
replies
3.0k
views
Enrichment Methods In Metagenomics
enrichment
analysis
metagenomics
updated 12 weeks ago by
Biostar
20 • written 9.7 years ago by
Dhruv Sakalley
▴ 110
0
votes
1
reply
153
views
Why are there soo many hits when using KOFAMSCAN?
annotation
protein
metagenomics
updated 3 months ago by
Mensur Dlakic
★ 10k • written 3 months ago by
O.rka
▴ 290
3
votes
0
replies
227
views
News:
ONLINE TRAINING: Environmental Metagenomics
assembly
metagenomics
nanopore
illumina
News
3 months ago by
carlopecoraro2
★ 2.0k
0
votes
2
replies
537
views
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
dqq102829
• 0 • written 15 months ago by
zhangdengwei
▴ 140
0
votes
2
replies
180
views
Where can get processed metagenome datasets?
metagenomics
sequencing
meta-genome
3 months ago by
m.koohi.m
▴ 120
0
votes
0
replies
204
views
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
views
Metagenomics - Functional analysis
metagenomics
megan
4 months ago by
lagartija
▴ 90
2
votes
3
replies
164
views
Embedding Metagenomics Tools onto a Website
metagenomics
bacteria
fungi
alignment
sequencing
updated 4 months ago by
Jean-Karim Heriche
24k • written 4 months ago by
stelaanag
• 0
0
votes
1
reply
172
views
Can I use metatranscriptomic reads for coverage when doing metagenomic binning?
metagenomics
metatranscriptomics
binning
updated 4 months ago by
Mensur Dlakic
★ 10k • written 4 months ago by
O.rka
▴ 290
3
votes
3
replies
390
views
Potential Bacteria Contamination - RNA-Seq
RNA-Seq
metagenomics
updated 5 months ago by
Thind amarinder
▴ 130 • written 8 months ago by
VHahaut
★ 1.1k
0
votes
0
replies
190
views
Remove certain species from standard database of Kraken
RNA-Seq
16s
kraken
bracken
metagenomics
updated 5 months ago by
Biostar
20 • written 5 months ago by
snishtala03
▴ 40
0
votes
4
replies
277
views
Preparing 16S gene amplicon (metagenomic) sequencing data for submission to ENA
16S
metagenomics
sequencing
ENA
updated 5 months ago by
antonioggsousa
★ 2.0k • written 5 months ago by
lyonskvn
• 0
3
votes
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
views
viral metagenomics classification: MINIMUM number of viral reads (cutoff) to consider a sample positive
metagenomics
classification
ngs
6 months ago by
Mania
• 0
1
vote
3
replies
234
views
memory allocation in metaSpades
spades
metagenomics
RAM
Assembly
updated 6 months ago by
GenoMax
99k • written 6 months ago by
Maorkn
• 0
0
votes
0
replies
224
views
Counting Biosyntheic Gene Clusters (BGC) types from Antismash Output
antismash
metagenomics
6 months ago by
arshad1292
▴ 40
18
votes
5
replies
7.2k
views
Open Source Sequence Assembly Programs
metagenomics
assembly
open
software
updated 6 months ago by
Biostar
20 • written 10.3 years ago by
Monzoor
▴ 300
2
votes
4
replies
212
views
mapping to incomplete reference
alignment
mapping
bowtie2
metagenomics
updated 6 months ago by
GenoMax
99k • written 6 months ago by
issia
• 0
0
votes
0
replies
257
views
How to normalize between samples in WGS metagenomics
Metagenomics
shotgun metagenomics
Normalization
6 months ago by
plicht
• 0
0
votes
0
replies
217
views
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
Biostar
20 • written 7 months ago by
Macspider
★ 3.4k
1
vote
0
replies
399
views
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
votes
10
replies
2.1k
views
Tools for metagenomics classification using long reads
metagenomics
sequen
alignment
updated 7 months ago by
bioinfo17
▴ 30 • written 3.0 years ago by
Medhat
8.9k
0
votes
6
replies
301
views
What are the input files for lwaldron / metaphlanToPhyloseq.R ?
r
metagenomics
metaphlan
updated 7 months ago by
zorbax
▴ 250 • written 7 months ago by
c.e.chong
▴ 40
1
vote
1
reply
398
views
Taxonomic classification of MAGs
metagenomics
genome
taxonomy
binning
updated 8 months ago by
Mensur Dlakic
★ 10k • written 8 months ago by
c.e.chong
▴ 40
2
votes
2
replies
258
views
What does "assembly-level" classification mean?
classifier
metagenomics
classification
updated 8 months ago by
h.mon
32k • written 8 months ago by
psun
• 0
1
vote
3
replies
282
views
Good Books/Resources to learn metagenomic analysis?
metagenomics
assembly
bacteria
nanopore
long reads
updated 8 months ago by
Mensur Dlakic
★ 10k • written 8 months ago by
jimpinney
▴ 10
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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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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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