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Are there "gold standard" datasets for identification of antibiotic resistance genes from metagenomic samples?
amr antibiotic resistance classification metagenomics
7 weeks ago by Bertalan_Takacs ▴ 100
3
votes
3
replies
497
views
Check if a BAM file is corrupt in Java
bam java
updated 3 months ago by 164k • written 4 months ago by ▴ 100
2
votes
1
reply
390
views
How to cluster microbial samples after principal coordinate analysis based on beta-diversity
clustering bray-curtis microbiome pcoa
updated 5 months ago by ★ 28k • written 5 months ago by ▴ 100
0
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1
reply
673
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Comment: Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
7 months ago by Bertalan_Takacs ▴ 100
0
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1
reply
673
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Comment: Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
7 months ago by Bertalan_Takacs ▴ 100
0
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5
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673
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Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 7 months ago by 147k • written 7 months ago by ▴ 100
0
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0
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1.7k
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Comment: Comment: esearch get taxonomy ID from a large list of accession IDs
8 months ago by Bertalan_Takacs ▴ 100
0
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0
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1.3k
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Comment: Comment: Precision-recall curve to compare metagenome classifiers to a gold standard - Is
15 months ago by Bertalan_Takacs ▴ 100
0
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0
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507
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I keep running into errors with the metagenomic classifer GOTTCHA. Can anybody offer some suggestions?
gottcha classification metagenomics
16 months ago by Bertalan_Takacs ▴ 100
3
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2
replies
1.4k
views
Subsetting DGEList object for for a list of genes of interest
dgelist transcriptomics subset edgeR
updated 2.0 years ago by 147k • written 2.0 years ago by ▴ 100
1
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0
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678
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Comment: Comment: What does the semicolon notation mean in proteomics analysis
2.0 years ago by Bertalan_Takacs ▴ 100
5
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2
replies
678
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What does the semicolon notation mean in proteomics analysis
differential expression semicolon proteomics analysis
2.0 years ago by Bertalan_Takacs ▴ 100
4
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4
replies
1.3k
views
Precision-recall curve to compare metagenome classifiers to a gold standard - Is this even a viable method?
classification recall precision metagenome
15 months ago by Bertalan_Takacs ▴ 100
0
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0
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458
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Microbiome beta-diversity: Bray-Curtis dissimilarity seems to be biased toward more diverse populations
bray-curtis beta-diversity microbiome classification dissimilarity
2.4 years ago by Bertalan_Takacs ▴ 100
0
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0
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370
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Immediate segmentation error when using STAR on SMART-Seq data
segmentation smart-seq dumped scRNA-seq STAR
2.5 years ago by Bertalan_Takacs ▴ 100
1
vote
1
reply
2.8k
views
Comment: Comment: barcode in the fastq files
2.5 years ago by Bertalan_Takacs ▴ 100
2
votes
1
reply
982
views
Galaxy error "FATAL: container creation failed"
cellranger galaxy pipeline containercreation scrna-seq
updated 2.5 years ago by 147k • written 2.5 years ago by ▴ 100
3
votes
1
reply
1.2k
views
Answer: Answer: Microbial community analysis pipelines in metagenomics
2.7 years ago by Bertalan_Takacs ▴ 100
5
votes
3
replies
4.9k
views
BLAST nr download and build - "nr.gz: invalid compressed data--format violated"
gzip nr BLAST
updated 20 months ago by 44k • written 2.8 years ago by ▴ 100
3
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1
reply
4.9k
views
Answer: Answer: BLAST nr download and build - "nr.gz: invalid compressed data--format violated"
2.7 years ago by Bertalan_Takacs ▴ 100
0
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0
replies
761
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Comment: Comment: How to threat bacterial genomes made up of multiple scaffolds in in silico metag
2.8 years ago by Bertalan_Takacs ▴ 100
2
votes
2
replies
761
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How to treat bacterial genomes made up of multiple scaffolds in in silico metagenome data generation
ncbi generation assembly metagenome insilico
2.8 years ago by Bertalan_Takacs ▴ 100
0
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3
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3.2k
views
Can't download files from the ENA (European Nucleotide Archive) site
ENA
updated 20 months ago by 44k • written 3.7 years ago by ▴ 100
1
vote
1
reply
1.0k
views
What is the best way for bacterial variant calling?
mutation prokaryote illumina variant calling
updated 3.4 years ago by 102k • written 3.4 years ago by ▴ 100
0
votes
0
replies
635
views
Generating random bed with interval lenghts following exponential distribution
length bed distribution intervals random
3.5 years ago by Bertalan_Takacs ▴ 100
0
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0
replies
756
views
A question about analyzing MACS2 outputs
broad-peak dropa drip-seq macs2
3.6 years ago by Bertalan_Takacs ▴ 100
0
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0
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3.2k
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Comment: A: Can't download files from the ENA (European Nucleotide Archive) site
3.7 years ago by Bertalan_Takacs ▴ 100
0
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0
replies
769
views
Reporting Kraken output in Sunbeam
metagenome sunbeam conda kraken2 multiqc
4.0 years ago by Bertalan_Takacs ▴ 100
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