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95 results • Page
1 of 2
Sort: Votes
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Views
Votes
Replies
3
votes
3
replies
469
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
2
votes
5
replies
448
views
Marking duplicates using UMIs
Deduplication
UMI
updated 3 days ago by
i.sudbery
19k • written 5 days ago by
Lipika
• 0
2
votes
5
replies
683
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 5 days ago by
Jesse
▴ 740 • written 6 days ago by
Ann
★ 2.4k
2
votes
4
replies
257
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
2 days ago by
samuelkalandarov2002
▴ 10
2
votes
9
replies
817
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
0
replies
75
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
16 hours ago by
rohitsatyam102
▴ 850
1
vote
2
replies
196
views
alignment result
RNA-seq
samtools
hisat2
1 day ago by
ahmad.sajad4541
• 0
1
vote
3
replies
244
views
some error in building kraken2 database
metagenome
kraken2
2 days ago by
Art1ess
• 0
1
vote
5
replies
260
views
Downsampling fastq file
downsample
fastq
updated 3 days ago by
Ram
43k • written 3 days ago by
marco.barr
▴ 80
1
vote
2
replies
231
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 18 days ago by
Netanel
• 0
1
vote
3
replies
205
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
2 days ago by
WouterDeCoster
47k
1
vote
1
reply
398
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
6 days ago by
renan.igor
• 0
1
vote
1
reply
163
views
Failed kmer content
kmer
illumina
ngs
updated 2 days ago by
Ram
43k • written 3 days ago by
Kasturi
• 0
1
vote
1
reply
413
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 5 days ago by
Gordon Smyth
★ 7.0k • written 7 days ago by
Chris
▴ 260
1
vote
0
replies
539
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
6 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
138
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 4 days ago by
Ram
43k • written 5 days ago by
sainavyav22
• 0
0
votes
2
replies
258
views
bam merging for archaic samples
samtools
bam
updated 4 days ago by
Ram
43k • written 5 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
125
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 4 days ago by
Carlo Yague
8.7k • written 4 days ago by
Atul K.
• 0
0
votes
0
replies
79
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
4 days ago by
Biostars2200
• 0
0
votes
0
replies
72
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
4 days ago by
sativus
▴ 20
0
votes
0
replies
90
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
3 days ago by
Enrique
• 0
0
votes
0
replies
72
views
Imputation advice
imputation
3 days ago by
kl
▴ 10
0
votes
0
replies
79
views
Annotating single cell data automatically
cell
annotation
single
3 days ago by
Gerard
• 0
0
votes
0
replies
82
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
3 days ago by
feather-W
• 0
0
votes
1
reply
148
views
RNA-seq bacteria contamination
RNA-seq
updated 3 days ago by
GenoMax
141k • written 3 days ago by
sh
• 0
0
votes
0
replies
84
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
3 days ago by
manaswwm
▴ 490
0
votes
1
reply
122
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 3 days ago by
ATpoint
82k • written 3 days ago by
enanoide
• 0
0
votes
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
3 days ago by
Javier
• 0
0
votes
1
reply
127
views
tbtool
tbtool
updated 3 days ago by
Ram
43k • written 3 days ago by
Raman
• 0
0
votes
2
replies
193
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
Patadu94
• 0
0
votes
0
replies
92
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 3 days ago by
Ram
43k • written 3 days ago by
sansan_96
▴ 80
0
votes
0
replies
195
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 3 days ago by
Ram
43k • written 3 days ago by
Oak
▴ 10
0
votes
0
replies
273
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 3 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
0
votes
0
replies
107
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 3 days ago by
Ram
43k • written 3 days ago by
maxime.policarpo
▴ 200
0
votes
1
reply
142
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 3 days ago by
Ram
43k • written 3 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
305
views
Error in cnetplot enrichplot package
R
updated 3 days ago by
Ram
43k • written 3 days ago by
Farhad
• 0
0
votes
0
replies
75
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
2 days ago by
alifafiq1
• 0
0
votes
0
replies
93
views
Merging replicates from Encode project
CHIP-seq
encode
2 days ago by
Nurken
• 0
0
votes
1
reply
152
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Srinka
▴ 20
0
votes
0
replies
87
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 2 days ago by
Ram
43k • written 2 days ago by
SHREYA
• 0
0
votes
0
replies
94
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 2 days ago by
Ram
43k • written 3 days ago by
Amélie
• 0
0
votes
1
reply
128
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 2 days ago by
bk11
★ 2.4k • written 2 days ago by
Susmita Mandal
▴ 110
0
votes
0
replies
93
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
2 days ago by
ohtang7
▴ 40
0
votes
0
replies
85
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 2 days ago by
Ram
43k • written 3 days ago by
SSSJec
• 0
0
votes
1
reply
150
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 2 days ago by
bk11
★ 2.4k • written 2 days ago by
alphaflylizard
• 0
0
votes
0
replies
103
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
2 days ago by
Kash
▴ 110
0
votes
1
reply
139
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
benguyarenbeyaz98
• 0
0
votes
6
replies
427
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 1 day ago by
gv
• 0 • written 24 days ago by
Srinka
▴ 20
0
votes
0
replies
127
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 day ago by
salias
• 0
95 results • Page
1 of 2
Recent Votes
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
Answer: Seurat merge and batch correction
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
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Recent Replies
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
ATpoint
82k
For question 1: For question 1: Purpose of indexing a genome/transcriptome/book/anything: https://www.biostars.org/p/212594/ For question …
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
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161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
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▴ 30
Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
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by
J
• 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
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161k
> using bcftools Show us what you tried
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22k
> Hi, guys, there is a question about the genomic gVCF file. I wonder > that since gVCF contains the non-var block records, why after merge…
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Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Comment: How to convert plink files to Hapmap Format
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These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
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So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
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by
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Thank you so much, it actually worked!
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