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questions
16
votes
26
replies
4.3k
views
13 follow
Genome Browser suggestions
Genome
Browser
GBrowse
IGV
Non-model
updated 2.4 years ago by
cmdcolin
★ 3.7k • written 6.6 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
632
views
Metaquast largest contig by species identical for most species in the metagenomic assembly
metagenomics
species
quast
contig
metaquast
2.9 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
611
views
Canu possibly idling in the "meryl" step
canu
meryl
assembly
genomics
kmer
3.0 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
1.1k
views
Displaying a controversial phylogenetic tree as a network to explicitate noise-generating branches
phylogenetic-tree
network
genome
updated 8 months ago by
Ram
43k • written 5.7 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
5
replies
2.0k
views
Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
GSEA
Escherichia coli
GO terms
gene set
RNA-Seq
updated 3.2 years ago by
Biostar
20 • written 3.3 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
3
replies
1.3k
views
How to convert E. coli gene names from biocyc to Ensembl IDs?
ENSEMBL
biocyc
Escherichia coli
conversion
R
updated 3.3 years ago by
Biostar
20 • written 3.3 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
1.0k
views
How to extract genes based on a list of GO terms or their children terms?
GOterms
Gene
Ontology
Children
Match
updated 3.4 years ago by
Biostar
20 • written 3.4 years ago by
Matteo Schiavinato
★ 3.6k
7
votes
2
replies
1.6k
views
DESeq2 design suggestions: one combined condition, or two separate conditions?
DESeq2
mRNAseq
rna-seq
R
Design
updated 3.5 years ago by
swbarnes2
14k • written 3.5 years ago by
Matteo Schiavinato
★ 3.6k
3
votes
13
replies
2.1k
views
RPKM and TPM when operating with small group of genes: is there a bias?
RPKM
TPM
RNASeq
Statistics
Sequencing
3.5 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
717
views
Performing so-called "SNP confirmation" for reads assigned to their corresponding Antibiotic Resistance Genes (ARGs): suggestions?
SNP
ARG
Reads
Megares
Metagenomics
updated 3.5 years ago by
Biostar
20 • written 3.5 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
4
replies
1.1k
views
Choice between Nanopore cDNA or direct RNA sequencing
nanopore
direct
RNA
cDNA
sequencing
3.7 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
3
replies
1.9k
views
Pipe pysam.view() output to pysam.sort()
pysam
sam
alignment
python
sort
updated 4.5 years ago by
gb
★ 2.2k • written 4.5 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
2
replies
2.2k
views
Extracting divergence times from 4DTv
variants
divergence
time
4DTv
substitution
updated 4.5 years ago by
Biostar
20 • written 5.3 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
618
views
Are GD format files (gdtools) 0-based?
genomediff
updated 12 months ago by
Ram
43k • written 4.6 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
11
replies
3.1k
views
How to annotate FASTA genome using GFF genes from another genome?
FASTA
GFF
annotation
program
genome
4.7 years ago by
Matteo Schiavinato
★ 3.6k
2
votes
2
replies
1.8k
views
Read position bias (RPB and PV4) fields from samtools mpileup: how to get them?
mpileup
variant
SNP
call
RPB
updated 4.9 years ago by
al.bodrug
▴ 50 • written 5.9 years ago by
Matteo Schiavinato
★ 3.6k
9
votes
5
replies
4.3k
views
CIGAR operations performed according to strand or to read?
read
sequencing
cigar
sam
format
updated 4.9 years ago by
shouldsee.gem
• 0 • written 6.3 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
6
replies
2.5k
views
ETE3 TreeError: 'Nodes are not connected!': how to fix?
ETE
phylome
phylogenetics
nodes
TreeError
5.2 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
2.9k
views
SplitsTree command line mode
SplitsTree
phylogeny
network
command line
pipeline
5.4 years ago by
Matteo Schiavinato
★ 3.6k
6
votes
6
replies
2.8k
views
CDS sequence from mRNA and protein sequence
FASTA
CDS
protein
mrna
code
updated 5.7 years ago by
lieven.sterck
15k • written 5.7 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
1.5k
views
Variant distance bias (VDB) in VCF format: how to compute properly?
vcf
Vdb
distance
bias
variant
5.9 years ago by
Matteo Schiavinato
★ 3.6k
2
votes
1
reply
2.4k
views
Converting blastn output to VCF (for SNPs): what is the quickest way?
VCF
blast
SNP
xml
updated 8 months ago by
Ram
43k • written 5.9 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
2
replies
1.2k
views
SNP/Mbp rate weird, any known bias/artifact?
SNP
Mbp
Variant
Calling
Bias
6.0 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
4
replies
1.5k
views
How do I tell bwa to map only unmapped portion of the read for supplementary alignments?
bwa
alignment
supplementary
SAM
chimeric
updated 6.3 years ago by
Pierre Lindenbaum
160k • written 6.3 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
1.3k
views
Can a part of a read be in the alignment and in the supplementary alignment (-F 0x800) as well?
sequencing
reads
chimeric
bwa
supplementary
6.3 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
1.0k
views
Whole-transcriptome RNASeq data of RNA-i engineered organism
RNA-Seq
RNAi
sequencing
transcriptome
transgene
6.4 years ago by
Matteo Schiavinato
★ 3.6k
7
votes
16
replies
2.7k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq
sequencing
updated 12 months ago by
Ram
43k • written 6.5 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
1.3k
views
Does it make sense to limit insert size when mapping on transcriptome?
RNA-seq
transcriptome
updated 12 months ago by
Ram
43k • written 6.5 years ago by
Matteo Schiavinato
★ 3.6k
2
votes
3
replies
2.5k
views
SAM Flags for illumina paired-end reads mapped on transcriptome
sam
flags
transcriptome
alignment
paired-end
updated 6.5 years ago by
Devon Ryan
104k • written 6.5 years ago by
Matteo Schiavinato
★ 3.6k
2
votes
0
replies
897
views
Subgenomes separation in hybrid species
Assembly
genome
sequencing
SNP
RNA-Seq
6.5 years ago by
Matteo Schiavinato
★ 3.6k
44
votes
4
replies
20k
views
Best way to compare two samples in a VCF file
VCF
Variant
Genotype
Comparison
SNP
updated 7 months ago by
Ram
43k • written 7.3 years ago by
Matteo Schiavinato
★ 3.6k
5
votes
1
reply
2.4k
views
How to retrieve Blast nr database dimensions?
Blast
Sequence
Nucleotide
Protein
Database
updated 6.7 years ago by
Sej Modha
5.3k • written 6.7 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
4
replies
1.8k
views
VCF Indel line structure: what is actually reported?
INDEL
VCF
Variant
Calling
SNP
updated 6.8 years ago by
Biostar
20 • written 7.0 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
2
replies
2.4k
views
Best set of nucmer mapping parameters for genome vs genome alignment
nucmer
nucleotide
alignment
genome
parameters
2.1 years ago by
Matteo Schiavinato
★ 3.6k
2
votes
9
replies
1.9k
views
GO Term enrichment with poor number of GO Terms
Gene Ontology
GO Terms
Annotation
InterPro
updated 6.9 years ago by
Jean-Karim Heriche
27k • written 6.9 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
3
replies
1.4k
views
Getting SNPs that are the complementary base of the reference
SNP
Variant
Calling
Alternative
Allele
7.1 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
4
replies
2.3k
views
Is Pindel slow for everyone, or should I review my command?
Pindel
Variant
Structural
Program
Detection
7.2 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
2.6k
views
Quality, MQ0F, other parameters for proper VCF filtering
SNP
alignment
genome
variant
VCF
7.2 years ago by
Matteo Schiavinato
★ 3.6k
12
votes
9
replies
19k
views
Remove duplicates from reads: best practices?
RNA-Seq
sequence
alignment
deduplication
next-gen
7.2 years ago by
Matteo Schiavinato
★ 3.6k
10
votes
10
replies
3.6k
views
HTSeq not counting all the fragments it should count on a gene
RNA-Seq
HTSeq
gene
expression
counts
7.3 years ago by
Matteo Schiavinato
★ 3.6k
17
votes
9
replies
5.2k
views
DESeq2 proper design setting
DESeq2
Differential Expression
Design
RNA-Seq
updated 7.3 years ago by
Carlo Yague
8.6k • written 7.3 years ago by
Matteo Schiavinato
★ 3.6k
4
votes
3
replies
2.2k
views
VCF Format INFO field: why do some keys in it not appear in the documentation?
VCF
SNP
Variants
Format
Calling
updated 7.3 years ago by
Pierre Lindenbaum
160k • written 7.3 years ago by
Matteo Schiavinato
★ 3.6k
6
votes
8
replies
2.2k
views
Why does bcftools call show variants with genotype 0/0 ?
genotype
reference
bcftools call
variant calling
7.4 years ago by
Matteo Schiavinato
★ 3.6k
43 results • Page
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