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Showing top results for tag: metagenomics • reset
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103
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How to normalize gene abundance from long read metagenomic data?
normalization metagenomics long-read gene-abundance
3 days ago by Adrián • 0
1
vote
3
replies
194
views
Unable to register for MG-RAST
metagenomics MG-RAST
updated 3 days ago by 146k • written 4 days ago by ▴ 10
0
votes
0
replies
150
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News: Upcoming November Courses – Enhance Your Skills in Bioinformatics and Data Analysis
Population-Genomics scRNA-seq RNA-seq Metagenomics Genome-Assembly
10 days ago by carlopecoraro2 ★ 2.6k
0
votes
2
replies
230
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Contig dereplication script not retrieving correct number of sequences
phage ANI metagenomics dereplication
13 days ago by bksakdinan.12 • 0
0
votes
0
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246
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Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
metagenomics taxonomy mag annotation
20 days ago by LuciaNhu • 0
0
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0
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438
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Are there "gold standard" datasets for identification of antibiotic resistance genes from metagenomic samples?
amr antibiotic resistance classification metagenomics
24 days ago by Bertalan_Takacs ▴ 100
1
vote
4
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328
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Problems with Megahit wanting to overwrite the Input for the output directory
metagenomics megahit slurm
updated 29 days ago by 164k • written 29 days ago by • 0
0
votes
0
replies
133
views
Annotating WGS Metagenome assemblies
metagenomics assembly metagenome annotation
4 weeks ago by naveedhasan2000 ▴ 10
1
vote
2
replies
411
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Track file for the DADA2 pipelne
microbiome-analysis metagenomics dada2 16s-amplicon
5 weeks ago by naveedhasan2000 ▴ 10
0
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0
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201
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News: Online course - Shotgun Metagenomics: Processing and Analysis
Prokka MetaPhlAn Metagenomics StrainPhlan PanPhlAn
updated 9 weeks ago by 44k • written 9 weeks ago by ★ 2.6k
0
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0
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238
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Job: Freelance Expert in Human Skin Microbiome
multiomics skin-microbiome metagenomics microbiota
updated 9 weeks ago by 44k • written 9 weeks ago by • 0
0
votes
0
replies
129
views
What to do with ALDEx2 associations where p < 0.05, but the 95% confidence intervals bridge zero
Metagenomics ALDEx2 Differential-abundance
updated 10 weeks ago by 44k • written 10 weeks ago by • 0
1
vote
5
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512
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Centrifuge Index creation issue
metagenomics centrifuge
10 weeks ago by skbrimer ▴ 740
1
vote
2
replies
263
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Remove specific reads from a metagenomic sequencing run
metagenomics
updated 11 weeks ago by 6.8k • written 11 weeks ago by ▴ 130
2
votes
3
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329
views
Confusion during BARCODE MATCHING.
primers metagenomics barcode
updated 11 weeks ago by 146k • written 11 weeks ago by • 0
2
votes
2
replies
402
views
Whole Metagenome Analysis
Metagenomics
11 weeks ago by karthick ▴ 10
1
vote
6
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521
views
Last against ncbi nr database
metagenomics virus alignment
10 weeks ago by Md Moinuddin • 0
4
votes
2
replies
690
views
Tool to align metagenomic data to reference genome
metagenomics alignment
updated 12 weeks ago by 6.8k • written 17 months ago by ▴ 10
0
votes
2
replies
269
views
Source code of metaCV
metagenomics metaCV
12 weeks ago by yeah • 0
2
votes
5
replies
474
views
MetaTranscriptomics amount of viable reads
metagenomics rna-seq transcriptomics
updated 3 months ago by 3.8k • written 3 months ago by • 0
0
votes
1
reply
302
views
Absolute counts or relative abundance for BC distance matrix
metagenomics microbiome
3 months ago by mail2steff ▴ 70
0
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1
reply
247
views
How do I Download Metagenomics Data from NCBI or EBI with its Metadata?
metagenomics NCBI
updated 3 months ago by 44k • written 3 months ago by ▴ 10
0
votes
2
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323
views
Building a Kraken2 Database
Taxonomy Kraken2 Metagenomics
updated 3 months ago by 44k • written 3 months ago by • 0
0
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0
replies
196
views
Calculation of RPM and deduplication
normalization metagenomics RPM deduplication
3 months ago by Luca Arbore • 0
0
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0
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243
views
News: ONLINE COURSE – Introduction to Metabarcoding and Metagenomics Analysis (IMAM01)
Metabarcoding Metagenomics
updated 4 months ago by 146k • written 4 months ago by ▴ 110
0
votes
1
reply
357
views
Understanding Discrepancies in Deduplication Rates Between Forward and Reverse Reads in Metagenomic Data
metagenomics deduplicate
updated 4 months ago by 44k • written 4 months ago by ▴ 20
2
votes
1
reply
549
views
Tool: Just released VEBA 2.0 in Nucleic Acids Research, a modular genome-resolved metagenomics/metatranscriptomics software suite that can handle prokaryot…
metatranscriptomics metagenomics microbiome veba
4 months ago by O.rka ▴ 740
2
votes
2
replies
454
views
Reformatting Fastq to Fasta for Metagenomic Analysis
metagenomics fasta fastq
updated 4 months ago by 6.8k • written 4 months ago by ▴ 20
0
votes
0
replies
179
views
Centrifuge Classifying Reads, but the Report is Empty
metagenomics centrifuge
updated 4 months ago by 146k • written 4 months ago by ▴ 20
0
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0
replies
233
views
Value of short kmer lengths with 300PE sequencing
metagenomics sequencing spades microbiome
4 months ago by Bryan ▴ 10
0
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0
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193
views
Why Does Metalign Relative Abundance Change?
metagenomics metalign
4 months ago by echolley ▴ 20
1
vote
0
replies
592
views
Job: [UK] Bioinformatics Programmer (Visa sponsored)
nextflow galaxy genomes bacterial metagenomics
4 months ago by µbinfie ▴ 20
0
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3
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572
views
Kraken2 Custom Database non-deterministic results
Metagenomics kraken2
updated 5 months ago by 6.8k • written 5 months ago by • 0
0
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0
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238
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics bacteria wgs AMR resistome
updated 5 months ago by 146k • written 5 months ago by • 0
0
votes
0
replies
298
views
Job: PhD position for metagenomics analysis at the University of Udine
metagenomics
updated 5 months ago by 44k • written 5 months ago by ★ 3.0k
0
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0
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247
views
Tera-scale metagenomic coassembly tool
co-assembly Metagenomics
5 months ago by Moinuddin • 0
0
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0
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268
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification Metagenomics Krona Kraken2
5 months ago by Aytaç • 0
0
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0
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212
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Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria Metagenomics Database
5 months ago by Christopher ▴ 10
0
votes
0
replies
254
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What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics metacyc enzyme pathway genomics
6 months ago by O.rka ▴ 740
0
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0
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228
views
Are some metagenomes too complex for MAGs?
metagenomics metagenome MAGs assembly
6 months ago by Jacob • 0
0
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1
reply
300
views
metagenomic virome quality assessment
viromics metagenomics
updated 6 months ago by 44k • written 6 months ago by • 0
1
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3
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647
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Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology metagenomics database enzymes genomics
updated 6 months ago by ★ 28k • written 6 months ago by ▴ 740
3
votes
4
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2.7k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 6 months ago by • 0 • written 2.9 years ago by • 0
2
votes
1
reply
479
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun metagenomics blastp taxonomy
updated 6 months ago by 146k • written 6 months ago by • 0
0
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2
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481
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics metacyc enzyme biobakery humann
6 months ago by O.rka ▴ 740
0
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0
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248
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Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization Metagenomics
updated 6 months ago by 44k • written 6 months ago by • 0
0
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2
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607
views
Azure vs AWS for cloud computing with Kraken2?
aws azure metagenomics kraken2
written 14 months ago by • 0
4
votes
4
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825
views
Bowtie2 mapping is slow
metagenomics bowtie2 mapping read
updated 6 months ago by 6.8k • written 7 months ago by • 0
0
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7
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993
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Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 4 months ago by • 0 • written 7 months ago by ▴ 20
31
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14
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12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna rRNA metagenomics
updated 7 months ago by 44k • written 14.0 years ago by ▴ 650
50 results • Page 1 of 1
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Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data by king • 0
Thank you for your answer, it's very inspiring.
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Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once? by GenoMax 146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
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The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
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I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type by allingt • 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
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The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
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Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation? by allingt • 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA? by allingt • 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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