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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
98
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
3 days ago by
S
• 0
0
votes
2
replies
203
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 3 days ago by
ATpoint
78k • written 3 days ago by
wangjb702
• 0
0
votes
0
replies
94
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 3 days ago by
Ram
41k • written 3 days ago by
aswin
• 0
0
votes
4
replies
277
views
Filling gaps in BAM file
bamtools
samtools
gene
bam
updated 2 days ago by
seidel
11k • written 3 days ago by
hemr3
• 0
0
votes
1
reply
148
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
3 days ago by
enriquesan
• 0
1
vote
5
replies
312
views
vcftools
vcftools
updated 3 days ago by
Barista
▴ 10 • written 3 days ago by
sevda
• 0
0
votes
0
replies
83
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
3 days ago by
cyril-cros
▴ 940
0
votes
1
reply
143
views
Microbial gene coverage from blast result
gene
coverage
3 days ago by
aanchal.yadav
• 0
0
votes
0
replies
89
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
3 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
103
views
Funannotate iprscan Creates empty file
funannotate
interproscan
fungus
annotation
3 days ago by
Umer
▴ 50
2
votes
2
replies
221
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
3 days ago by
hkarakurt
▴ 180
0
votes
4
replies
663
views
How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
genome
threader
2 days ago by
peanut
• 0
2
votes
5
replies
244
views
kallisto index build difference according to version
index
version
kallisto
updated 4 days ago by
dsull
★ 5.1k • written 4 days ago by
estilo
• 0
0
votes
2
replies
519
views
Understanding gene level copy number data from TCGAbiolinks
CNV
TCGA
updated 4 days ago by
Zhenyu Zhang
★ 1.1k • written 13 months ago by
billyK
• 0
1
vote
3
replies
338
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 4 days ago by
GenoMax
136k • written 4 days ago by
bkffadia
• 0
0
votes
0
replies
118
views
Should I perform eQTL colocalization for just one of eGenes at a time?
colocalization
coloc
eCaviar
eQTL
5 days ago by
maximal_life
▴ 20
4
votes
2
replies
275
views
KEGG DATABASE
DATABASE
KEGG
updated 2 days ago by
jv
★ 1.3k • written 5 days ago by
Sijjil
• 0
0
votes
1
reply
216
views
Issue with genetic QC sex check
plink
6 days ago by
kl
▴ 10
0
votes
0
replies
117
views
BioSQL Unable to remove database using server.remove_database
BioSQL
biopython
Mysql
Python
6 days ago by
Navindu
• 0
0
votes
0
replies
129
views
bootstraped treemix show no migration event
Treemix
Bootstrap
6 days ago by
reza
▴ 300
0
votes
2
replies
1.5k
views
Does GNOMAD use all LOFTEE LoF filters?
loftee
gnomad
LOF
ensembl
vep
updated 6 days ago by
AMARU
• 0 • written 3.8 years ago by
brismiller
▴ 50
0
votes
3
replies
813
views
"MethylKit" package for WGBS data
MethylKit
WGBS
updated 6 days ago by
viveksomya123
• 0 • written 2.4 years ago by
shrinka.genetics
▴ 20
0
votes
0
replies
150
views
is there a way to set colors pallets for glMDSPlot(x)?
Glimma
glMDSPlot
6 days ago by
James
• 0
0
votes
0
replies
135
views
Compute matrix skipping many regions stating not found in compute matrix output
computematrix
Deeptools
6 days ago by
Mehwish
▴ 10
0
votes
0
replies
205
views
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
promoter
motif
updated 3 days ago by
Ram
41k • written 6 days ago by
shome
▴ 10
0
votes
2
replies
260
views
How to identify CG, CHG, or CHH from MeDIP data
MethylationStudy
CHG
CHH
CG
MeDIP
3 days ago by
Tm
★ 1.1k
0
votes
0
replies
160
views
Significance of several BUSCO target IDs for the same gene
target_id
sequence-ontology
BUSCO
duplication
6 days ago by
CoLa
• 0
0
votes
1
reply
211
views
doubt about usage of megahit
trinity
megahit
updated 6 days ago by
Istvan Albert
99k • written 7 days ago by
meera
• 0
0
votes
0
replies
149
views
Osmotic permeability of water transport in aquaporins
permeability
Osmotic
transport
Water
7 days ago by
Peerzada
• 0
0
votes
1
reply
452
views
Loftee no splice site annotations
Loftee
VEP
updated 7 days ago by
AMARU
• 0 • written 21 months ago by
Filago
▴ 90
0
votes
0
replies
132
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
7 days ago by
luckyday1661
• 0
0
votes
1
reply
179
views
How to get multiple protein domain database domain name from id's
annotations
blast2go
domain
domains
proteins
updated 7 days ago by
GenoMax
136k • written 7 days ago by
Nicolas
• 0
0
votes
0
replies
149
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
7 days ago by
Ty
• 0
0
votes
1
reply
200
views
Annotate Unplaced Scaffold with Chromosome Information
assembly
annotation
scaffold
Chromosome
updated 7 days ago by
cmdcolin
★ 3.4k • written 7 days ago by
Trevor
• 0
0
votes
0
replies
133
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
7 days ago by
bioinfo
▴ 140
0
votes
3
replies
266
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 7 days ago by
Istvan Albert
99k • written 7 days ago by
Jingfang
• 0
0
votes
1
reply
158
views
PAML Troubleshooting Help
PAML
codeml
updated 7 days ago by
dthorbur
▴ 890 • written 8 days ago by
sebabiokr
▴ 10
0
votes
0
replies
104
views
how to calculate intramodular connectivity
WGCNA
intramodularConnectivity
8 days ago by
hellokwmin
• 0
2
votes
2
replies
218
views
R script in docker
R
Visual_studio_code
Docker
7 days ago by
mrashad
▴ 70
0
votes
0
replies
98
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE
admixture
8 days ago by
maxlaubstein
• 0
0
votes
5
replies
303
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
updated 3 days ago by
manaswwm
▴ 490 • written 8 days ago by
J
• 0
0
votes
0
replies
130
views
GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data
mouse
GATK
Mutect2
dbSNP
8 days ago by
luckyday1661
• 0
0
votes
2
replies
339
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 8 days ago by
fracarb8
★ 1.3k • written 8 days ago by
synat.keam
▴ 80
3
votes
6
replies
479
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 6 days ago by
jv
★ 1.3k • written 8 days ago by
newbee
▴ 40
0
votes
0
replies
126
views
deeptools k-means clustering
heatmap
deeptools
chipseq
8 days ago by
biology_inform
▴ 50
0
votes
1
reply
172
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
updated 8 days ago by
Nitin Narwade
★ 1.5k • written 8 days ago by
tss243
• 0
6
votes
3
replies
270
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 8 days ago by
Jeremy
▴ 860 • written 8 days ago by
ohtang7
▴ 40
0
votes
0
replies
107
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 8 days ago by
GenoMax
136k • written 8 days ago by
sativus
▴ 10
0
votes
0
replies
124
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 8 days ago by
GenoMax
136k • written 8 days ago by
PierreGT
• 0
0
votes
0
replies
117
views
sequencing deep mutational scanning library
mutagenesis
illumina
long-read
sequencing
8 days ago by
reaset41
• 0
1,000 results • Page
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Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: how to remove multiple columns from a file in R
Answer: how to remove multiple columns from a file in R
Answer: Read count vs Depth
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Comment: Normalization of RNA captureSeq data (<20 genes captured)
by
ATpoint
78k
What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
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j.gleixner
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Since all your sequences have the same length (say M) and you are only looking concerned with hamming distance you can encode your sequence…
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Thank you very much! I see you decided to go for Bowtie as aligner. Do you see any issue in using STAR (as a splice aware reader technicall…
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Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
Pierre Lindenbaum
158k
again, it's a problem with the variant caller, which is ?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Not only opposite case but same case nucleotides are also present in vcf fle. ![enter image description here][1] [1]: /media/images/4…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Yes [Pierre][1] there is lower case **g** in **REF** and upper case **G** in **ALT** field. My question is that why variant caller is calli…
Answer: gatk SelectVariants is giving error while extracting SNPs out of vcf file
by
Pierre Lindenbaum
158k
This is an error in your input vcf file. The REF allele MUST be différent from the ALT allele.
Comment: gatk SelectVariants is giving error while extracting SNPs out of vcf file
by
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I observed that my reference genomic fasta file contains both lower case and upper case nucleotides. Do I need to convert lower case nucle…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
I observed that both lower and upper cases are present in reference fasta file. Is bbtool case sensitive that while calling variants it con…
Comment: Read count vs Depth
by
Mary
• 0
Thanks Brain Bushnell Referring to my query1: So u mean that for a particular gene, if total read count is 6, then depth may be just 1 or …
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