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0
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replies
4.6k
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Answer:
Answer: Is there a way to use CNVkit without a reference from normal samples?
13 months ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
38k
views
Comment:
Comment: Any tools converting Genbank format to GFF3 format?
2.2 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
2.6k
views
Comment:
Comment: Best set of nucmer mapping parameters for genome vs genome alignment
2.7 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
7.7k
views
Comment:
Comment: Converting MUMmer snps file to a real VCF file
2.8 years ago by
Matteo Schiavinato
★ 3.6k
5
votes
8
replies
7.7k
views
6 follow
Tool:
Converting MUMmer snps file to a real VCF file
VCF
mummer
SNP
updated 16 months ago by
Ram
44k • written 5.2 years ago by
Matteo Schiavinato
★ 3.6k
16
votes
26
replies
4.8k
views
13 follow
Genome Browser suggestions
Genome
Browser
GBrowse
IGV
Non-model
updated 3.0 years ago by
cmdcolin
★ 4.0k • written 7.2 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
639
views
Tool:
Manticore: a software to extract the intermixed regions of subgenomes in hybrid species
mapping
hybrid
subgenome
genomics
sequencing
3.3 years ago by
Matteo Schiavinato
★ 3.6k
3
votes
1
reply
1.4k
views
Tool:
all2vcf: a tool to convert non-standard variant outputs (mummer. bcftools isec) to VCF
mummer
isec
variant
bcftools
VCF
updated 2.0 years ago by
ayeshatariq78
• 0 • written 3.3 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
725
views
Metaquast largest contig by species identical for most species in the metagenomic assembly
metagenomics
species
quast
contig
metaquast
3.5 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
701
views
Canu possibly idling in the "meryl" step
canu
meryl
assembly
genomics
kmer
3.6 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
1.2k
views
Displaying a controversial phylogenetic tree as a network to explicitate noise-generating branches
phylogenetic-tree
network
genome
updated 16 months ago by
Ram
44k • written 6.3 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
5
replies
2.5k
views
Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
GSEA
Escherichia coli
GO terms
gene set
RNA-Seq
updated 3.8 years ago by
Biostar
20 • written 3.9 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
3
replies
1.5k
views
How to convert E. coli gene names from biocyc to Ensembl IDs?
ENSEMBL
biocyc
Escherichia coli
conversion
R
updated 3.9 years ago by
Biostar
20 • written 3.9 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
1.5k
views
Comment:
C: How to convert E. coli gene names from biocyc to Ensembl IDs?
3.9 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
2.5k
views
Comment:
C: Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
3.9 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
2.5k
views
Comment:
C: Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
3.9 years ago by
Matteo Schiavinato
★ 3.6k
2
votes
0
replies
661
views
Answer:
A: how can I the unwanted fasta sequences?
3.9 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
1.2k
views
Comment:
C: How I can get all the information of proteins?
3.9 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
10k
views
Comment:
C: Remove part of headers in FASTA file
3.9 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
1.1k
views
How to extract genes based on a list of GO terms or their children terms?
GOterms
Gene
Ontology
Children
Match
updated 4.0 years ago by
Biostar
20 • written 4.0 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
19k
views
Comment:
C: DESeq2: "model matrix is not full rank"
4.0 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
19k
views
Answer:
A: DESeq2: "model matrix is not full rank"
4.0 years ago by
Matteo Schiavinato
★ 3.6k
7
votes
2
replies
1.9k
views
DESeq2 design suggestions: one combined condition, or two separate conditions?
DESeq2
mRNAseq
rna-seq
R
Design
updated 4.1 years ago by
swbarnes2
14k • written 4.1 years ago by
Matteo Schiavinato
★ 3.6k
4
votes
1
reply
4.4k
views
Answer:
A: python calculation of protein multiple sequence alignment
4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
2.5k
views
Comment:
C: SPAdes v3.14 unable to find files despite correct file path
4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
4.1k
views
Comment:
C: Filtering low quality score bases from BAM file
4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
2.5k
views
Comment:
C: SPAdes v3.14 unable to find files despite correct file path
4.1 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
2.5k
views
Comment:
C: SPAdes v3.14 unable to find files despite correct file path
4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
2.5k
views
Comment:
C: SPAdes v3.14 unable to find files despite correct file path
4.1 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
4.1k
views
Comment:
C: Filtering low quality score bases from BAM file
4.1 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
4.1k
views
Answer:
A: Filtering low quality score bases from BAM file
4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
2.6k
views
Comment:
C: RPKM and TPM when operating with small group of genes: is there a bias?
4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
2.6k
views
Comment:
C: RPKM and TPM when operating with small group of genes: is there a bias?
4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
2.6k
views
Comment:
C: RPKM and TPM when operating with small group of genes: is there a bias?
4.1 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
2.6k
views
Comment:
C: RPKM and TPM when operating with small group of genes: is there a bias?
4.1 years ago by
Matteo Schiavinato
★ 3.6k
3
votes
13
replies
2.6k
views
RPKM and TPM when operating with small group of genes: is there a bias?
RPKM
TPM
RNASeq
Statistics
Sequencing
4.1 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
2.6k
views
Answer:
A: RPKM and TPM when operating with small group of genes: is there a bias?
4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
2.6k
views
Comment:
C: RPKM and TPM when operating with small group of genes: is there a bias?
4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
2.6k
views
Comment:
C: RPKM and TPM when operating with small group of genes: is there a bias?
4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
791
views
Performing so-called "SNP confirmation" for reads assigned to their corresponding Antibiotic Resistance Genes (ARGs): suggestions?
SNP
ARG
Reads
Megares
Metagenomics
updated 4.1 years ago by
Biostar
20 • written 4.1 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
2.7k
views
Comment:
C: kraken2table, an analogous to kaiju2table
4.3 years ago by
Matteo Schiavinato
★ 3.6k
4
votes
4
replies
2.7k
views
Tool:
kraken2table, an analogous to kaiju2table
kaiju
classification
kraken
taxonomy
updated 16 months ago by
Ram
44k • written 4.3 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
2.7k
views
Comment:
C: kraken2table, an analogous to kaiju2table
4.3 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
1.3k
views
Comment:
C: Choice between Nanopore cDNA or direct RNA sequencing
4.4 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
1.3k
views
Comment:
C: Choice between Nanopore cDNA or direct RNA sequencing
4.4 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
4
replies
1.3k
views
Choice between Nanopore cDNA or direct RNA sequencing
nanopore
direct
RNA
cDNA
sequencing
4.4 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
2.9k
views
Comment:
C: ETE3 TreeError: 'Nodes are not connected!': how to fix?
4.4 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
1
reply
7.7k
views
Comment:
C: Converting MUMmer snps file to a real VCF file
4.5 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
1.7k
views
Comment:
C: Extract allele read counts for heterozygous positions in VCF
5.1 years ago by
Matteo Schiavinato
★ 3.6k
2
votes
1
reply
1.7k
views
Answer:
A: Extract allele read counts for heterozygous positions in VCF
5.1 years ago by
Matteo Schiavinato
★ 3.6k
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