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121,524 results • Page
624 of 2431
Sort: Rank
Rank
Views
Votes
Replies
4
votes
9
replies
2.5k
views
randomly sampling long read data for genome assembly
pacbio
assembly
genome
4.1 years ago by
jleehan
▴ 120
3
votes
8
replies
3.8k
views
Correlation plot
Correlation
R
corrplot
updated 4.1 years ago by
Arsenal
▴ 160 • written 4.1 years ago by
Rob
▴ 180
3
votes
5
replies
1.2k
views
6 follow
What genes are mutated in Lukemia?
Lukemia
updated 4.1 years ago by
seidel
11k • written 4.1 years ago by
Fatemehrazmjoyi
• 0
2
votes
4
replies
3.4k
views
TCGA Sample barcode
Tumor
Barcode
Normal
TCGA
updated 4.1 years ago by
Cyriac Kandoth
6.1k • written 4.1 years ago by
manjumoorthy95
▴ 60
0
votes
1
reply
671
views
combine metagenomic assemblies using cat?
Assembly
updated 4.1 years ago by
andres.firrincieli
3.9k • written 4.1 years ago by
goatsrunfaster
▴ 60
0
votes
5
replies
1.1k
views
Find sequence/variants from ancient-DNA genomes
DNA
ancient
updated 4.1 years ago by
4galaxy77
2.9k • written 4.1 years ago by
alexandrerouen
• 0
4
votes
12
replies
2.5k
views
Multifactor Design For RNA-seq Analysis
Rna-seq
batch
correction
DESeq2
multifactor
4.1 years ago by
David Martínez
▴ 10
2
votes
2
replies
1.1k
views
Best hit from BLAST for a particular genomic region
genomic
blast
region
best
hit
evalue
updated 4.1 years ago by
Alex Reynolds
36k • written 4.1 years ago by
johnny.sf
▴ 20
3
votes
4
replies
1.9k
views
Proportion of RNAseq reads mapping to rRNA, tRNA, mRNA, and intergenic or antisense regions of the genome?
GTF
featureCounts
NGS
GFF
updated 4.1 years ago by
i.sudbery
21k • written 4.1 years ago by
mathavanbioinfo
▴ 80
12
votes
9
replies
7.0k
views
Good annotation databases for a VCF file (somatic variants)
VCF
ANNOVAR
somatic
databases
annotation
updated 4.0 years ago by
emma.a
▴ 130 • written 4.1 years ago by
Zahra
▴ 110
8
votes
9
replies
2.1k
views
superimpose
discovery
ds
visualizer
4.1 years ago by
Alex
▴ 20
0
votes
2
replies
941
views
X-transposed region on chromosome Y
chromosome-X
CNV
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
alexandrerouen
• 0
0
votes
0
replies
600
views
How to run PWM scan with hundreds of PWM at the same time?
PWMScan
ATAC-seq
PWMtools
4.1 years ago by
juanpjlozano
• 0
0
votes
7
replies
1.8k
views
How to increase the number of matched sequences in blastn
mismatch
blastn
updated 4.1 years ago by
Dunois
★ 2.9k • written 4.1 years ago by
jahanshahi.amin
• 0
1
vote
6
replies
2.0k
views
Unable to update Rstudio
updateR
updated 4.1 years ago by
ATpoint
88k • written 4.1 years ago by
Kira
• 0
0
votes
0
replies
1.5k
views
HOMER annotatepeaks.pl
ChIP-Seq
HOMER
sequencing
next-gen
4.1 years ago by
jjp55
▴ 20
3
votes
4
replies
2.4k
views
6 follow
Segmentation fault in bcftools while changing the sample names
vcftools
bcftools
updated 4.1 years ago by
GenoMax
152k • written 4.3 years ago by
kumar.vinod81
▴ 340
3
votes
6
replies
1.8k
views
Convert sam file with no header to fastq
fastq
sam
gatk
updated 4.1 years ago by
ATpoint
88k • written 4.1 years ago by
daewowo
▴ 80
2
votes
3
replies
1.1k
views
Splice site impact
sites
Splice
updated 4.1 years ago by
Emily
24k • written 4.1 years ago by
Jng
• 0
0
votes
3
replies
1.2k
views
mapping with bfast killed when created index
bfast
mapping
index
updated 4.1 years ago by
JC
13k • written 4.1 years ago by
Lila M
★ 1.3k
0
votes
1
reply
1.1k
views
How to view large PPI network in STRING database?
PPI
large
network
STRING
updated 4.1 years ago by
Jean-Karim Heriche
27k • written 4.1 years ago by
mathavanbioinfo
▴ 80
6
votes
12
replies
5.0k
views
Trim bam file reads to remove all nucleotide over a certain length
bam
trimming
updated 4.1 years ago by
GenoMax
152k • written 4.1 years ago by
Juke34
9.2k
47
votes
22
replies
38k
views
17 follow
Multi-Sample Vcf To Phylogenetic Tree.
vcf
updated 13 months ago by
RT
• 0 • written 11.8 years ago by
William
★ 5.4k
1
vote
2
replies
1.7k
views
bcftools filter
filter
bcftools
4.1 years ago by
Gregor Rot
▴ 550
0
votes
2
replies
1.5k
views
A USER ERROR has occurred: Bad input: the IUPAC sample specified is not present in the provided VCF file
GATK
IUPAC
CONSENSUS
VCF
FastaAlternateReferenceMaker
4.1 years ago by
Vanuhi
• 0
0
votes
0
replies
570
views
Motif search in protein list
interactome
motif
search
batch
4.1 years ago by
florian.roehrig
• 0
3
votes
5
replies
2.4k
views
STAR Genome index could not open genomeFastaFile
RNAseq
genome
alignment
STAR
4.1 years ago by
bs58
▴ 10
14
votes
4
replies
4.0k
views
Exclusion Of Regions In Cnv Analysis
plink
updated 2.9 years ago by
Ram
45k • written 13.0 years ago by
bob.obr13n
▴ 60
2
votes
7
replies
1.6k
views
Count the numfer of reads supporting a pattern from a BAM file
samtools
updated 4.1 years ago by
jkbonfield
★ 1.3k • written 4.1 years ago by
User000
▴ 750
11
votes
2
replies
6.1k
views
OrthoFinder: Diamond or Blast? Which is better?
orthofinder
blast
sensitivity
ortholog
updated 3.3 years ago by
Dunois
★ 2.9k • written 4.1 years ago by
greyman
▴ 190
2
votes
4
replies
2.0k
views
Bray Curtis for functional dissimilarity
dissimilarity
bray
curtis
updated 4.1 years ago by
Kevin Blighe
89k • written 4.1 years ago by
statisticsnovice
• 0
0
votes
0
replies
638
views
how to use circos plot to plot euchromation and heterochromatin
perl
circos
plot
4.1 years ago by
szp770
▴ 10
0
votes
0
replies
582
views
Annotations for ReadDepth
CNVs
NGS
ReadDepth
4.1 years ago by
ICfc97
▴ 20
0
votes
1
reply
2.1k
views
Differential Gene Expression Analysis From TMM normalized counts
RNA-Seq
updated 4.1 years ago by
Gordon Smyth
★ 8.2k • written 6.0 years ago by
boyinepallyki
• 0
9
votes
8
replies
8.2k
views
TMM - Normalized FPKM values for RNASeq data ?
RNA-Seq
next-gen
R
updated 4.1 years ago by
Gordon Smyth
★ 8.2k • written 9.1 years ago by
gangireddy
▴ 160
2
votes
0
replies
978
views
What rate of heterozygosity is considered low or high in a plant genome assembly?
heterozygosity
assembly
genome
plant
4.1 years ago by
resug
▴ 40
1
vote
0
replies
577
views
Full protein sequence or only conserved domains
proteins
phylogenetics
4.1 years ago by
Vasiliy Krestov
▴ 30
3
votes
1
reply
1.5k
views
canonical transcript from vep
ensembl
transcript
appris
canonical
tsl
updated 4.1 years ago by
Emily
24k • written 4.1 years ago by
romain.lannes
▴ 90
0
votes
0
replies
789
views
DE analysis with Ballgown; what are DE genes produced from data containing three groups
DGE
R
Ballgown
updated 4.1 years ago by
ATpoint
88k • written 4.1 years ago by
Annika
• 0
1
vote
1
reply
1.4k
views
What is the correct way of setting the genotype after splitting multi-allelic sites in a VCF file?
genotype
bcftools
vcf
updated 4.1 years ago by
Kevin Blighe
89k • written 4.1 years ago by
terdon
▴ 430
0
votes
0
replies
705
views
Nx3 chromosome intrnaction matrix into NxN
matrix
hic
4.1 years ago by
Oleczkaff
• 0
0
votes
2
replies
1.0k
views
Viral taxonomic classification question
taxonomic-classification
viral-metagenomics
4.1 years ago by
v.berriosfarias
▴ 140
2
votes
3
replies
2.5k
views
Ambiguous SNPs
SNPs
updated 4.1 years ago by
Emily
24k • written 4.1 years ago by
nhaus
▴ 420
0
votes
5
replies
1.4k
views
How to compare pathway significances after treatment?
pathway
significance
comparison
4.1 years ago by
Cancan
• 0
2
votes
2
replies
1.2k
views
How to obtain all PDB IDs containing similar binding sites with a specific ligand
protein
PDB
ligand
site
binding
Binding
4.1 years ago by
antoniaa
▴ 30
0
votes
0
replies
834
views
Convert different types of databases to ANNOVAR custom databases
ANNOVAR
CIViC
DoCM
annotation
VCF
4.1 years ago by
Zahra
▴ 110
4
votes
6
replies
1.6k
views
RNA-seq for beginners
reference
resequencing
transcriptome
gtf
sequence
gff
4.1 years ago by
arko.bmb.du
▴ 20
57
votes
5
replies
27k
views
6 follow
How do you generate TMM normalized counts using EdgeR?
R
RNA-seq
edgeR
updated 15 months ago by
inedraylig
▴ 70 • written 4.1 years ago by
Pratik
★ 1.1k
1
vote
5
replies
1.6k
views
filtering dataframe using multiple columns in R
filter
R
dataframe
updated 4.1 years ago by
Ram
45k • written 4.1 years ago by
andreiareis1987
▴ 40
2
votes
5
replies
3.4k
views
Difference between KO and ko numbers?
pathway
updated 4.1 years ago by
andres.firrincieli
3.9k • written 4.1 years ago by
deep771992chanda
▴ 40
121,524 results • Page
624 of 2431
Recent Votes
Answer: NCBI Datasets CLI Question
Answer: NCBI Datasets CLI Question
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
Answer: NCBI Datasets CLI Question
SNP calling with SAMtools on multiple samples
Comment: Crac: Funny And/Or Weird Names For Bioinformatics Tools
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Zev.Kronenberg
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152k
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Comment: Which Reference Hg38 or T2T?? Both??
by
Jon
• 0
![enter image description here][1] [1]: /media/images/7880cb6b-9bae-4506-8f27-380a5515 This is one of the examples I'm talking about. …
Comment: Which Reference Hg38 or T2T?? Both??
by
Jon
• 0
The reference I'm having issues is the Naegleria Fowleri Karachi NF001, as this is the one that shows up in my samples. Everything I have …
Answer: Which Reference Hg38 or T2T?? Both??
by
GenoMax
152k
> So if I have my human sample and remove reads matching T2T, that Should? give me a host free set of reads??? For purpose of host deconta…
Comment: NCBI Datasets CLI Question
by
Bjorn
• 0
Thanks! Works great.
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
by
louisflower1999
• 0
Hi GenoMax, Thanks so much for your suggestion! Those amplicons are around 4.4kb. And there should be at least 1kb from the left and 800 b…
Comment: NCBI Datasets CLI Question
by
GenoMax
152k
Wanted to make it a complete answer with an additional command. Moved now.
Comment: NCBI Datasets CLI Question
by
Mensur Dlakic
★ 29k
Maybe make this an answer rather than a comment?
Comment: PCA interpretation
by
swbarnes2
15k
You are trying to PCA these by what, exactly? Binned coverage? Is this really informative?
Answer: NCBI Datasets CLI Question
by
GenoMax
152k
I don't see a way to specify a random number of accessions to download as an option. Perhaps you may want to open an issue and suggest that…
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
by
Zev.Kronenberg
12k
@genomax has a good point about trying `pbaa`. The tool will output consensus sequences of the different alleles. You can then use MSA to a…
Answer: Joint Calling for Large Germline WGS Cohort
by
Jeremy Leipzig
23k
Not to get too pedantic but joint genotyping solves a different problem (removing artefactual variants) from producing a population VCF tha…
Answer: Joint Calling for Large Germline WGS Cohort
by
DBScan
▴ 490
Another option would be HAILs VDS Combiner, [https://hail.is/docs/0.2/vds/hail.vds.combiner.VariantDatasetCombiner.html#hail.vds.combiner.V…
Comment: how shoud the phred score be intepreted?
by
QX
▴ 70
thank you for explanation and documentation
Comment: how shoud the phred score be intepreted?
by
GenoMax
152k
Illumina sequencing assumes/generally expects that clusters in a sequencing field have an even distribution of ACTG so for every sequencing…
Comment: how shoud the phred score be intepreted?
by
QX
▴ 70
what do you mean by 'low nucleotide diversity'. If it is low nucleotide diversity, is it supposed to have consistent signals, leading to hi…
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