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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
263
views
Annovar using R package
Annovar
gnomAD
R
8 days ago by
DKA
▴ 40
0
votes
5
replies
370
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 8 days ago by
GenoMax
142k • written 9 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
148
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 9 days ago by
Ram
43k • written 9 days ago by
glaciya2018
• 0
0
votes
0
replies
311
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
9 days ago by
pramach1
▴ 40
0
votes
1
reply
171
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 9 days ago by
Sofia
• 0 • written 9 days ago by
mawigoj318
• 0
0
votes
0
replies
149
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
9 days ago by
salias
• 0
0
votes
5
replies
366
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 6 days ago by
Istvan Albert
100k • written 9 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
128
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 9 days ago by
Ram
43k • written 9 days ago by
newuser2024
• 0
1
vote
2
replies
247
views
alignment result
RNA-seq
samtools
hisat2
8 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
118
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
9 days ago by
Kash
▴ 110
0
votes
1
reply
167
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 9 days ago by
Mensur Dlakic
★ 27k • written 10 days ago by
benguyarenbeyaz98
• 0
2
votes
2
replies
297
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 9 days ago by
Ram
43k • written 10 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
878
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 9 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
11
replies
596
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
7 days ago by
atowns21
• 0
0
votes
1
reply
180
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 10 days ago by
bk11
★ 2.4k • written 10 days ago by
alphaflylizard
• 0
0
votes
0
replies
104
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
10 days ago by
ohtang7
▴ 40
0
votes
1
reply
179
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 10 days ago by
GenoMax
142k • written 10 days ago by
Srinka
▴ 20
0
votes
5
replies
360
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
9 days ago by
njornet
▴ 20
0
votes
0
replies
102
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 10 days ago by
Ram
43k • written 10 days ago by
SHREYA
• 0
0
votes
0
replies
110
views
Merging replicates from Encode project
CHIP-seq
encode
10 days ago by
Nurken
• 0
1
vote
3
replies
254
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
10 days ago by
WouterDeCoster
47k
1
vote
3
replies
296
views
some error in building kraken2 database
metagenome
kraken2
9 days ago by
Art1ess
• 0
0
votes
1
reply
177
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 10 days ago by
bk11
★ 2.4k • written 10 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
187
views
Failed kmer content
kmer
illumina
ngs
updated 10 days ago by
Ram
43k • written 10 days ago by
Kasturi
• 0
0
votes
0
replies
98
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 10 days ago by
Ram
43k • written 10 days ago by
SSSJec
• 0
0
votes
1
reply
154
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 11 days ago by
Ram
43k • written 11 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
376
views
Error in cnetplot enrichplot package
R
updated 11 days ago by
Ram
43k • written 11 days ago by
Farhad
• 0
0
votes
0
replies
115
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 11 days ago by
Ram
43k • written 11 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
102
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 11 days ago by
Ram
43k • written 11 days ago by
sansan_96
▴ 80
0
votes
0
replies
105
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 10 days ago by
Ram
43k • written 11 days ago by
Amélie
• 0
0
votes
0
replies
211
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 11 days ago by
Ram
43k • written 11 days ago by
Oak
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 11 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
1
vote
8
replies
459
views
Downsampling fastq file
downsample
fastq
3 days ago by
marco.barr
▴ 90
0
votes
1
reply
146
views
tbtool
tbtool
updated 11 days ago by
Ram
43k • written 11 days ago by
Raman
• 0
0
votes
10
replies
499
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
i.sudbery
19k • written 11 days ago by
Patadu94
• 0
0
votes
1
reply
138
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 11 days ago by
ATpoint
82k • written 11 days ago by
enanoide
• 0
0
votes
0
replies
94
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
11 days ago by
manaswwm
▴ 510
0
votes
0
replies
84
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
10 days ago by
alifafiq1
• 0
0
votes
0
replies
90
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
11 days ago by
feather-W
• 0
2
votes
4
replies
324
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
9 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
90
views
Annotating single cell data automatically
cell
annotation
single
11 days ago by
Gerard
• 0
0
votes
1
reply
172
views
RNA-seq bacteria contamination
RNA-seq
updated 11 days ago by
GenoMax
142k • written 11 days ago by
sh
• 0
0
votes
0
replies
81
views
Imputation advice
imputation
11 days ago by
kl
▴ 10
0
votes
0
replies
102
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
11 days ago by
Enrique
• 0
0
votes
0
replies
82
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
11 days ago by
sativus
▴ 20
0
votes
0
replies
87
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
11 days ago by
Biostars2200
• 0
0
votes
0
replies
141
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 11 days ago by
Carlo Yague
8.7k • written 11 days ago by
Atul K.
• 0
2
votes
5
replies
484
views
Marking duplicates using UMIs
Deduplication
UMI
updated 11 days ago by
i.sudbery
19k • written 12 days ago by
Lipika
• 0
0
votes
0
replies
145
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 12 days ago by
Ram
43k • written 12 days ago by
sainavyav22
• 0
0
votes
0
replies
150
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
12 days ago by
rthapa
▴ 90
1,000 results • Page
3 of 20
Recent Votes
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
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Recent Awards •
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SHN
▴ 40
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Rob
▴ 170
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to
GenoMax
142k
Popular Question
to
curious
▴ 750
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M.
▴ 30
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carolofharvest
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e.r.zakiev
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Answer: visualize GSEA
by
bk11
★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Mbofire
• 0
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Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
by
e.r.zakiev
▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
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