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5.2k
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Answer: Answer: Is there a way to use CNVkit without a reference from normal samples?
20 months ago by Matteo Schiavinato ★ 3.7k
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0
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40k
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Comment: Comment: Any tools converting Genbank format to GFF3 format?
2.8 years ago by Matteo Schiavinato ★ 3.7k
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0
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2.9k
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Comment: Comment: Best set of nucmer mapping parameters for genome vs genome alignment
3.3 years ago by Matteo Schiavinato ★ 3.7k
0
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1
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8.8k
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Comment: Comment: Converting MUMmer snps file to a real VCF file
3.4 years ago by Matteo Schiavinato ★ 3.7k
5
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8
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8.8k
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6 follow
Tool: Converting MUMmer snps file to a real VCF file
VCF mummer SNP
updated 2.0 years ago by 45k • written 5.8 years ago by ★ 3.7k
16
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26
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5.7k
views
13 follow
Genome Browser suggestions
Genome Browser GBrowse IGV Non-model
updated 3.6 years ago by ★ 4.2k • written 7.8 years ago by ★ 3.7k
0
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0
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740
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Tool: Manticore: a software to extract the intermixed regions of subgenomes in hybrid species
mapping hybrid subgenome genomics sequencing
3.9 years ago by Matteo Schiavinato ★ 3.7k
3
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1
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1.8k
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Tool: all2vcf: a tool to convert non-standard variant outputs (mummer. bcftools isec) to VCF
mummer isec variant bcftools VCF
updated 2.6 years ago by • 0 • written 3.9 years ago by ★ 3.7k
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0
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907
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Metaquast largest contig by species identical for most species in the metagenomic assembly
metagenomics species quast contig metaquast
4.1 years ago by Matteo Schiavinato ★ 3.7k
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0
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826
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Canu possibly idling in the "meryl" step
canu meryl assembly genomics kmer
4.2 years ago by Matteo Schiavinato ★ 3.7k
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0
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1.3k
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Displaying a controversial phylogenetic tree as a network to explicitate noise-generating branches
phylogenetic-tree network genome
updated 23 months ago by 45k • written 6.9 years ago by ★ 3.7k
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5
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3.0k
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Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
GSEA Escherichia coli GO terms gene set RNA-Seq
updated 4.5 years ago by 20 • written 4.6 years ago by ★ 3.7k
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3
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1.8k
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How to convert E. coli gene names from biocyc to Ensembl IDs?
ENSEMBL biocyc Escherichia coli conversion R
updated 4.5 years ago by 20 • written 4.5 years ago by ★ 3.7k
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1
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1.8k
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Comment: C: How to convert E. coli gene names from biocyc to Ensembl IDs?
4.5 years ago by Matteo Schiavinato ★ 3.7k
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1
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3.0k
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Comment: C: Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
4.6 years ago by Matteo Schiavinato ★ 3.7k
0
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1
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3.0k
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Comment: C: Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
4.6 years ago by Matteo Schiavinato ★ 3.7k
2
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0
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770
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Answer: A: how can I the unwanted fasta sequences?
4.6 years ago by Matteo Schiavinato ★ 3.7k
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1
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1.5k
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Comment: C: How I can get all the information of proteins?
4.6 years ago by Matteo Schiavinato ★ 3.7k
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0
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11k
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Comment: C: Remove part of headers in FASTA file
4.6 years ago by Matteo Schiavinato ★ 3.7k
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0
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1.3k
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How to extract genes based on a list of GO terms or their children terms?
GOterms Gene Ontology Children Match
updated 4.6 years ago by 20 • written 4.6 years ago by ★ 3.7k
2
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1
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22k
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Comment: C: DESeq2: "model matrix is not full rank"
4.6 years ago by Matteo Schiavinato ★ 3.7k
1
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1
reply
22k
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Answer: A: DESeq2: "model matrix is not full rank"
4.6 years ago by Matteo Schiavinato ★ 3.7k
7
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2
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2.4k
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DESeq2 design suggestions: one combined condition, or two separate conditions?
DESeq2 mRNAseq rna-seq R Design
updated 4.7 years ago by 15k • written 4.7 years ago by ★ 3.7k
4
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1
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5.2k
views
Answer: A: python calculation of protein multiple sequence alignment
4.7 years ago by Matteo Schiavinato ★ 3.7k
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0
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3.0k
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
4.7 years ago by Matteo Schiavinato ★ 3.7k
0
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1
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5.1k
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Comment: C: Filtering low quality score bases from BAM file
4.7 years ago by Matteo Schiavinato ★ 3.7k
0
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1
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3.0k
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
4.7 years ago by Matteo Schiavinato ★ 3.7k
1
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1
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3.0k
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
4.7 years ago by Matteo Schiavinato ★ 3.7k
0
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1
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3.0k
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Comment: C: SPAdes v3.14 unable to find files despite correct file path
4.7 years ago by Matteo Schiavinato ★ 3.7k
1
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1
reply
5.1k
views
Comment: C: Filtering low quality score bases from BAM file
4.7 years ago by Matteo Schiavinato ★ 3.7k
1
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1
reply
5.1k
views
Answer: A: Filtering low quality score bases from BAM file
4.7 years ago by Matteo Schiavinato ★ 3.7k
0
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0
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3.3k
views
Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
4.7 years ago by Matteo Schiavinato ★ 3.7k
0
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1
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3.3k
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Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
4.7 years ago by Matteo Schiavinato ★ 3.7k
0
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1
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3.3k
views
Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
4.7 years ago by Matteo Schiavinato ★ 3.7k
1
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1
reply
3.3k
views
Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
4.7 years ago by Matteo Schiavinato ★ 3.7k
3
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13
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3.3k
views
RPKM and TPM when operating with small group of genes: is there a bias?
RPKM TPM RNASeq Statistics Sequencing
4.7 years ago by Matteo Schiavinato ★ 3.7k
1
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1
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3.3k
views
Answer: A: RPKM and TPM when operating with small group of genes: is there a bias?
4.7 years ago by Matteo Schiavinato ★ 3.7k
0
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0
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3.3k
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Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
4.7 years ago by Matteo Schiavinato ★ 3.7k
0
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0
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3.3k
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Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
4.7 years ago by Matteo Schiavinato ★ 3.7k
0
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0
replies
914
views
Performing so-called "SNP confirmation" for reads assigned to their corresponding Antibiotic Resistance Genes (ARGs): suggestions?
SNP ARG Reads Megares Metagenomics
updated 4.7 years ago by 20 • written 4.8 years ago by ★ 3.7k
0
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0
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3.2k
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Comment: C: kraken2table, an analogous to kaiju2table
4.9 years ago by Matteo Schiavinato ★ 3.7k
6
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4
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3.2k
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Tool: kraken2table, an analogous to kaiju2table
kaiju classification kraken taxonomy
updated 2.0 years ago by 45k • written 4.9 years ago by ★ 3.7k
0
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1
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3.2k
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Comment: C: kraken2table, an analogous to kaiju2table
4.9 years ago by Matteo Schiavinato ★ 3.7k
0
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0
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1.6k
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Comment: C: Choice between Nanopore cDNA or direct RNA sequencing
5.0 years ago by Matteo Schiavinato ★ 3.7k
0
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0
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1.6k
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Comment: C: Choice between Nanopore cDNA or direct RNA sequencing
5.0 years ago by Matteo Schiavinato ★ 3.7k
1
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4
replies
1.6k
views
Choice between Nanopore cDNA or direct RNA sequencing
nanopore direct RNA cDNA sequencing
5.0 years ago by Matteo Schiavinato ★ 3.7k
0
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0
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3.4k
views
Comment: C: ETE3 TreeError: 'Nodes are not connected!': how to fix?
5.0 years ago by Matteo Schiavinato ★ 3.7k
0
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1
reply
8.8k
views
Comment: C: Converting MUMmer snps file to a real VCF file
5.1 years ago by Matteo Schiavinato ★ 3.7k
0
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0
replies
2.1k
views
Comment: C: Extract allele read counts for heterozygous positions in VCF
5.7 years ago by Matteo Schiavinato ★ 3.7k
2
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1
reply
2.1k
views
Answer: A: Extract allele read counts for heterozygous positions in VCF
5.7 years ago by Matteo Schiavinato ★ 3.7k
600 results • Page 1 of 12
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